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# Applied Marine Sciences, Inc.

Aquatic and Marine Environmental Sciences

## Sitemaps

- [XML Sitemap](https://amarine.com/sitemap.xml): Contains all public & indexable URLs for this website.

## Posts

- [Our Santa Cruz office has moved!](https://amarine.com/our-santa-cruz-office-has-moved/) - Please note that our new address is: 303 Potrero St. Ste 42-304 Santa Cruz, CA 95060
- [AMS Participates in Expedition to Davidson Seamount](https://amarine.com/ams-participates-in-expedition-to-davidson-seamount/) - AMS supported Monterey Bay National Marine Sanctuary on a recent expedition to Davidson Seamount approximately 55 miles off the central California coast aboard E/V Nautilus, operated by Ocean Exploration Trust. AMS installed a pump and sampling media on the ROV Hercules to perform in situ solid-phase extraction of water and collect sediment cores for measurement
- [AMS publication recognized as top downloaded article](https://amarine.com/ams-publication-recognized-as-top-downloaded-article/) - Mine Berg and Sara Driscoll's 2017 publication, Variation in growth rate, carbon assimilation, and photosynthesis efficiency in response to nitrogen source and concentration in phytoplankton isolated from upper San Francisco Bay, was the top downloaded article in 2017-2018 and one of the top 20 most read papers from the peer-reviewed Journal of Phycology. Amongst articles
- [AMS Awarded GSA Contract](https://amarine.com/ams-awarded-gsa-contract/) - AMS was awarded a GSA contract in 2019 for SINs 899-1 / 899-1RC (Environmental Consulting Services), 899-7 / 899-7RC (Geographic Information System (GIS)), and 00CORP-500 / 00CORP500RC (Order-Level Materials (OLMs)). Please contact Paul Salop for any inquiries related to this award. On-line access to contract ordering information, terms, and conditions, up-to-date pricing, and the option to
- [New Publication: Effects of Nitrogen and Irradiance on Growth of Two Diatoms](https://amarine.com/effects-of-nitrogen-and-irradiance-on-growth-of-two-diatoms-endemic-to-suisun-bay/) - AMS’ most recent publication evaluates the importance of light versus nutrients in driving phytoplankton growth in San Francisco Bay which has an excess of nutrients relative to the requirement for phytoplankton growth. As nutrients have not traditionally been considered as important as light for regulating phytoplankton biomass in San Francisco Bay, we investigated the role
- [Microbial Source Tracking Project in Monterey Bay](https://amarine.com/microbial-source-tracking/) - AMS is conducting a project using microbial source tracking (MST) to trace anthropogenic (i.e. from humans or their domestic animals) sources of fecal indicator bacteria (FIBs), and to quantify their importance relative to wildlife fecal bacteria sources, in ocean receiving waters along the Central California coast. This project uses quantitative polymerase chain reaction (qPCR) probes
- [Innovation in San Francisco Bay Monitoring](https://amarine.com/innovation-in-san-francisco-bay-monitoring/) - AMS deployed acoustic release devices (Edge Tech’s PORT-MF Pop-Ups) at seven locations in San Francisco Bay in support of the Regional Monitoring Program’s bioaccumulation program. As part of this biennial effort, AMS deployed cages containing transplanted bivalves, secured by the acoustic release devices to weights that hold them in position at pre-determined locations. The releases,
- [Central Coast Long-term Environmental Assessment Network (CCLEAN)](https://amarine.com/central-coast-long-term-environmental-assessment-network-cclean/) - CCLEAN has been tracking concentrations of persistent organic pollutants (POPs) in Monterey Bay since 2004. Annual average concentrations of polychlorinated biphenyls (PCBs), in particular, have exceeded the California Ocean Plan water quality objective in nearly 10 out of 12 years. Recent results have shown that fluctuations in annual average PCB concentrations are highly correlated with
- [Areas of Special Biological Significance in California](https://amarine.com/areas-of-special-biological-significance-in-california/) - AMS recently completed a study of stormwater discharges into Areas of Special Biological Significance (ASBS) on the California coast from Big Sur to Marin County. This involved comparison of pollutant concentrations in ocean waters receiving stormwater discharges with ocean waters at the mouths of undeveloped watersheds. Results from the study supported innovative analytical approaches for determining
- [Mine Berg and Sara Driscoll publish on Ammonium in San Francisco Bay Phytoplankton Communities](https://amarine.com/mine-berg-and-sara-driscoll-publish-on-ammonium-in-san-francisco-bay-phytoplankton-communities/) - The northern part of San Francisco Bay is home to the endangered Delta Smelt and intersects the migratory routes of many pelagic fish species including salmon. Unfortunately, this region poses a number of stressors for the organisms that live there including changes in water flows and hydrology, water temperature, turbidity and contaminants resulting from agriculture
- [Plankton and Clam Research for Regional San](https://amarine.com/nutrients-and-phytoplankton-research-for-regional-san/) - The Sacramento River is the largest river in California and travels 400 miles from the Klamath Mountains in Oregon to San Francisco Bay. Together with scientists from Regional San, AMS scientists sample 16 stations along a 76-mile stretch between river mile 95 (north of the Feather River confluence) and river mile 19 (north of Rio
- [Supporting San Francisco Infrastructure Upgrades](https://amarine.com/supporting-san-francisco-infrastructure-upgrades/) - The San Francisco Public Utilities Commission (SFPUC) is in the early stages of a 20-year, multi-billion dollar capital improvement program intended to upgrade its wastewater infrastructure. The Sewer System Improvement Project (SSIP) includes investigation of projects with potential to improve the water quality of San Francisco Bay by altering the frequency, location, and duration of
- [AMS Investigates Nutrient Dynamics in the Suisun Bay-Delta](https://amarine.com/ams-investigates-nutrient-dynamics-in-the-suisun-bay-delta/) - AMS has been actively engaged in supporting dischargers, regulatory agencies, and the research community in interpreting the effects of recent changes in nutrient dynamics in the Suisun Bay-Delta on phytoplankton growth and ecosystem health. As part of our efforts, Dr. Mine Berg has supported development of a conceptual model on nutrients in the Bay-Delta, participated
- [Bioaccumulation Monitoring in San Francisco Bay](https://amarine.com/bioaccumulation-monitoring-in-san-francisco-bay/) - AMS has been conducting long-term bioaccumulation monitoring in San Francisco Bay in support of the San Francisco Estuary Institute’s Regional Monitoring Program for Water Quality in the San Francisco Estuary. Equipment and images from this investigation will be included in an exhibit at the Oakland Museum of California entitled "Above and Below: Stories From Our

## Pages

- [Home](https://amarine.com/) - AMS is a California-certified, Small Business Enterprise with state-wide offices in Livermore and Santa Cruz, California.
- [Career Opportunities](https://amarine.com/careers/) - Join Our Team AMS is not currently accepting applications at this time. Please continue to check our LinkedIn page and website for future job opportunities. Oceanographer/Marine Scientist Applied Marine Sciences, Inc. (AMS) has an immediate opening for a highly motivated mid-level Oceanographer / Marine Scientist to join our staff. The position allows the successful candidate
- [Contact Us](https://amarine.com/contact/) - Contact Us Corporate Headquarters 4749 Bennett Dr., Ste LLivermore, CA 94551925-373-7142 (phone)925-373-7834 (fax)Email Paul Salop Santa Cruz Office 303 Potrero St. Ste 42-304 Santa Cruz, CA 95060831-426-6326 (phone)Email Aroon Melwani
- [Staff](https://amarine.com/staff/) - Staff AMS’ professional staff has a broad range of experience, capabilities, and expertise. With more than 150 years combined experience in providing marine, aquatic and environmental consulting services, company principals and staff have expertise in marine biology, aquatic chemistry, oceanography, toxicology, fisheries, limnology, biogeochemistry, computer sciences, data management, and modeling. Moreover, AMS’ network of professional associates
- [Our Commitment to Web Accessibility](https://amarine.com/accessibility-statement/) - Our Commitment to Web Accessibility Applied Marine Sciences, Inc. is committed to providing a fully accessible website experience for all users of all abilities, including those who rely on assistive technologies like screen readers, screen enlargement software, and alternative keyboard input devices to navigate the web. Ongoing Efforts to Ensure Accessibility We follow the Web Content
- [About](https://amarine.com/about/) - About Us Applied Marine Sciences (AMS) is a small, science-based consulting firm with a proven track record in the environmental field. AMS began in 1989, as a direct result of its efforts to support the assessment and remediation of sensitive ecosystems impacted by the Exxon Valdez oil spill. Since its inception, AMS has expanded to
- [Regulatory Compliance Monitoring](https://amarine.com/regulatory-compliance-monitoring/) - AMS performs accurate and effective environmental analyses based on a thorough understanding of applicable national and state regulations.
- [Energy and Infrastructure](https://amarine.com/energy-and-infrastructure/) - Energy and Infrastructure AMS Supports Large-Scale Energy and Infrastructure Projects in Aquatic Environments AMS has provided an important service in supporting large-scale energy and infrastructure projects planned and executed in and around the aquatic environment. We have worked for project developers, natural resource management, and regulatory agencies to ensure that project design and implementation are
- [Environmental Program Management](https://amarine.com/environmental-program-management/) - Environmental Program Management AMS Uses Science-Based Inquiry to Support Sound Decision Making in Multi-Stakeholder Processes AMS personnel work at the nexus of science and policy and have an extensive history of using science-based inquiry to support sound decision making in multi-stakeholder processes. Our management strategy utilizes a comprehensive understanding of local, state, federal, and international
- [News](https://amarine.com/news/) - News Find out what’s new at AMS Explore a few of the company’s highlights past and present. Follow us on LinkedIn for regular updates on our work.
- [Publications](https://amarine.com/publications-2/) - Publications
- [Projects](https://amarine.com/projects/) - Projects AMS conducts a wide array of projects to improve management of aquatic systems in California and beyond. Since 1989, AMS has designed and implemented monitoring strategies, tools and approaches to support the protection, management, and enhancement of the coastal ocean, estuaries, and the watersheds that drain into them. Ecological Assessment Energy & Infrastructure Water
- [Publications - New NAme](https://amarine.com/publications-robert-spies-2/) - Featured Documents: New Name
- [Privacy Policy](https://amarine.com/privacy-policy/) - Privacy Policy This Website for Applied Marine Sciences, Inc. collects some Personal Data from its Users. Users may be subject to different protection standards and broader standards may therefore apply to some. In order to learn more about the protection criteria, Users can refer to the applicability section. Owner and Data Controller Applied Marine Sciences,
- [Water Quality Monitoring](https://amarine.com/water-quality-monitoring/) - Water Quality Monitoring AMS Conducts Long-Term Water Quality Monitoring Programs in San Francisco Bay and Central Coast of California AMS has been instrumental in the design, implementation, and management of several long-term water quality monitoring programs in the San Francisco Bay area and along the Central Coast of California. These programs assess the potential impacts
- [Ecological Assessments](https://amarine.com/ecological-assessment/) - AMS Provides Comprehensive Ecological Assessments to Track Ecosystem Behavior and Mitigate Anthropogenic Impacts Ecological assessments are essential for tracking ecosystem behavior, determining the magnitude of anthropogenic impacts and disturbances, assessing the performance of strategies for mitigating the effects of particular projects, and for documenting restoration efforts. AMS designs and implement studies across a wide variety
- [Services](https://amarine.com/services/) - Services AMS designs, conducts, and manages projects in marine, estuarine, and freshwater environments throughout California, nationally, and internationally. AMS projects involve complex biological and chemical phenomena, including fate and effects of chemical contaminants, biological contamination, and ecological baseline and impact monitoring assessments. AMS provides scientific support and project management to government agencies, coastal utilities, the
- [Publications - Robert Spies](https://amarine.com/publications-robert-spies/) - Featured Documents: Robert Spies
- [Publications - Jay Johnson](https://amarine.com/publications-jay-johnson/) - Featured Documents: Jay Johnson
- [Publications - Dane Hardin](https://amarine.com/publications-dane-hardin/) - Featured Documents: Dane Hardin
- [Publications - Paul Salop](https://amarine.com/publications-paul-salop/) - Featured Documents: Paul Salop
- [Publications - Aroon Melwani](https://amarine.com/publications-aroon-melwani/) - Featured Documents: Aroon Melwani

## Staff

- [Katerina Bischel](https://amarine.com/staff/katerina-bischel/) - Katerina Bischel is an environmental scientist specializing in water quality, contaminant fate and transport, and the application of machine learning and geospatial analysis to environmental monitoring. She earned her Master of Environmental Science and Management (M.E.S.M.) from the Bren School at the University of California, Santa Barbara in 2026, with concentrations in Pollution Prevention and Remediation and Water Resource Management.
- [Jackie Mohay](https://amarine.com/staff/jackie-mohay/) - Jackie Mohay is a Marine Scientist with over 15 years of experience in fisheries and conservation biology. Her work prior to joining AMS included working as a fisheries observer in the Bering Sea and Pacific Ocean, as well as monitoring the status of threatened and endangered species in the California Central Valley.
- [Aroon Melwani](https://amarine.com/staff/aroon-melwani/) - Aroon Melwani is a senior marine scientist specializing in experimental design, sample collection, and quantitative analysis of environmental data. He has over 16 years experience supporting local, regional and state agencies on sediment and water quality, contaminant bioaccumulation, and biological assessments. His technical expertise includes data management, statistical analysis, data integration, empirical modeling, and R programming.
- [Dane Hardin](https://amarine.com/staff/dane-hardin/) - Dane Hardin’s studies have a strong quantitative emphasis that involves use of data from numerous available sources to help explain variations in water quality measurements. He is the Executive Director of the Central Coast Long-term Environmental Assessment Network (CCLEAN), which is a regional water quality monitoring program in Monterey Bay, California. He also recently directed a large regional monitoring program to address discharges of stormwater in Areas of Special Biological Significance along the central California coast.
- [Robert Spies](https://amarine.com/staff/robert-spies/) - Bob Spies has 35 years experience in applied marine ecology and its application to management. He has investigated the fate and effects of radionuclides, petroleum hydrocarbons, and chlorinated hydrocarbons in marine ecosystems. Specific research projects conducted over his career have included investigations into the effects of organic contaminants on endocrinology and reproduction of starry flounder in San Francisco Bay and kelp bass in southern California.
- [Jay Johnson](https://amarine.com/staff/jay-johnson/) - Jay Johnson has over 30 years professional experience in applied marine and aquatic sciences, environmental consulting and program management. He has extensive experience in dealing with complex scientific regulatory and environmental issues, effectively interacting with local, state, national and international agencies, developing and implementing cost effective due diligence, baseline and impact monitoring programs and assessing and alleviating environmental impacts.
- [Ellen Goldenberg](https://amarine.com/staff/ellen-goldenberg/) - Ellen Goldenberg is a scientist specializing in temperate and tropical aquatic fish and benthic communities. Ms. Goldenberg earned an MS in Marine Biology from Nova Southeastern University in Fort Lauderdale, Florida where she worked as a full-time research assistant in the Coral Reef Restoration, Assessment and Monitoring Lab. She served as the first manager of the Broward County Nearshore Transects project, which is a long-term government funded effort designed to examine the impacts of beach nourishment on coastal benthic habitats in Southeast Florida.
- [Dovlynn Cammack](https://amarine.com/staff/dovlynn-cammack/) - Since joining AMS, Dovlynn Cammack has been active in office management, corporate insurance, staff resources, benefit administration and IT programs. Dovlynn specializes in accounting, financial reporting, income statements, balance sheets and budget development. She has performed logistics for field planning, equipment procurement and management, shipping of hazardous materials, and assisted in scientific collection efforts and transportation.
- [Paul Salop](https://amarine.com/staff/paul-salop/) - Paul Salop has over 15 years of experience working for consulting firms and state and Federal agencies. Paul is currently serving as Project Manager for AMS in its role supporting the Alameda Countywide Clean Water Program’s (ACCWP) stormwater monitoring and watershed management efforts, managing all field collection efforts and field quality control for the Status and Trends Component of the Regional Monitoring Program for Water Quality in the San Francisco Estuary.
- [Diane Stafford](https://amarine.com/staff/diane-stafford/) - At AMS, Diane Stafford specializes in the set-up and creation of detailed invoices tailored to meet client needs and performs monthly invoicing and accounts receivables. Diane is proficient in MS Excel and Word, and uses such to prepare monthly, quarterly, and annual reporting. She also handles insurance and compliance, expense reimbursements, business licensing and permits, logistics for field planning, equipment procurement and management

## Projects

- [Central Coast Long-term Environmental Assessment Network](https://amarine.com/projects/central-coast-long-term-environmental-assessment-network/) - CCLEAN is a long-term regional monitoring program that assists municipal agencies and resource managers in the fulfillment their roles as environmental stewards by providing information needed to protect the quality of nearshore marine waters in the Monterey Bay area. AMS led the effort to design the Central Coast Long-Term Environmental Assessment Network (CCLEAN) regional monitoring program.
- [Areas of Special Biological Significance](https://amarine.com/projects/areas-of-special-biological-significance-2/) - Areas of Special Biological Significance (ASBS) are areas designated by the California State Water Board that include marine life refuges, ecological reserves, and designated areas where the preservation and enhancement of natural resources requires special protection. These protections prevent discharges of waste, including stormwater. In 2012, revisions to the California Ocean Plan required stormwater dischargers in ASBS to fulfill new monitoring requirements.
- [Per- and Polyfluoroalkyl Substances (PFAS) in Wastewater](https://amarine.com/projects/per-and-polyfluoroalkyl-substances-pfas-in-wastewater/) - AMS assisted municipal participants in fulfilling PFAS monitoring requirements and provided a turn-key program that included designing a sampling plan, training on sample collection, and analysis using a specialized laboratory. AMS also managed data and assisted dischargers with understanding automated reports, minimizing staff time and securing volume discounts.
- [Monterey Bay Ocean Monitoring to Support CalAm’s Baseline Monitoring Requirements](https://amarine.com/projects/monterey-bay-ocean-monitoring-to-support-calams-baseline-monitoring-requirements/) - AMS has conducted monthly CTD water column profiles in Monterey Bay to gather a time-series of water conditions near the Monterey One Water wastewater outfall. AMS has also helped CalAm meet ocean monitoring and reporting requirements for the Monterey Peninsula Water Supply Project, a desalination project in the area.
- [Biological Monitoring Survey Design Review](https://amarine.com/projects/biological-monitoring-survey-design-review/) - AMS led a Monitoring Design Review under the direction of an interagency Steering Committee to examine opportunities to improve the design of five existing biological monitoring surveys in the San Francisco Bay-Delta to address current management needs. AMS was under contract to ICF through funding provided by the USBR, as the principal investigator on an evaluation and analysis of five biological monitoring surveys.
- [Central Coast Long-term Environmental Assessment Network (CCLEAN) Microplastics Pilot Study](https://amarine.com/projects/central-coast-long-term-environmental-assessment-network-cclean-microplastics-pilot-study/) - In 2020, AMS added microplastics sampling to the Central Coast Long-term Environmental Assessment Network (CCLEAN) program in the Monterey Bay area. AMS sampled for microplastics in effluent sources and rivers discharging into the bay during the wet and dry seasons of 2021. Controlled volumes of effluent and river water were passed through sieve systems to capture different sizes of microplastic particles.
- [CEQA Support for Proposed West Basin Municipal Water District Coastal Desalination Facility](https://amarine.com/projects/ceqa-support-for-proposed-west-basin-municipal-water-district-coastal-desalination-facility/) - AMS scientists characterized the existing marine biological resources and potential Project impacts, including sensitive and special-status species, within a portion of Santa Monica Bay on behalf of West Basin Municipal Water District for a proposed coastal desalination facility. The West Basin Municipal Water District, a wholesale water agency serving a number of municipalities, corporations, and
- [Alternative Ocean Wind and Wave Energy Projects](https://amarine.com/projects/alternative-ocean-wind-and-wave-energy-projects/) - AMS scientists have been actively involved in renewable ocean energy projects along the West Coast since 2008. AMS was contracted by ICF (the project lead) to support the US Department of Energy (DOE) for their mobile ocean renewable energy testing berth offshore Central Oregon and operated by Oregon State University. AMS provided marine habitat, biota,
- [RTI-Manchester Beach Fiber Optic Cable Project Marine Resources and Route Characterization Reports](https://amarine.com/projects/rti-manchester-beach-fiber-optic-cable-project-marine-resources-and-route-characterization-reports/) - AMS prepared a detailed assessment and characterization of marine seafloor habitats and associated biological communities along two fiber optic cable routes through nearshore waters offshore of Manchester, California. In the past two decades, increased demand for trans-Pacific communications have resulted in installation of dozens of new fiber optic cables terminating in the California coastal zone.
- [Compliance Monitoring for Oceanic Fiber Optic Cable Landings in Eureka, California](https://amarine.com/projects/compliance-monitoring-for-oceanic-fiber-optic-cable-landings-in-eureka-california/) - AMS was contracted by RTI to provide State-mandated monitoring of three Horizontal Directionally Drilled (HDD) landfalls of Trans-Pacific submarine fiber optic cable systems in Eureka, California. In the past two decades, increased demand for trans-Pacific communications has resulted in the installation of dozens of new fiber optic cables terminating in the California coastal zone. Each
- [Decommissioning of the Pacific Refining Marine Oil Terminal](https://amarine.com/projects/decommissioning-of-the-pacific-refining-marine-oil-terminal/) - AMS provided CEQA support and third-party independent environmental mitigation monitoring assessments at the abandoned Pacific Refining marine oil terminal. Pacific Refining decommissioned and abandoned their refinery in Hercules, CA, in 1997, and left the supporting marine oil terminal (MOT) located in San Pablo Bay in caretaker status. Plans to permanently abandon and remove the terminal
- [Implementation of the EPA Water Quality Improvement Grant Project, Clean Watersheds for a Clean Bay](https://amarine.com/projects/implementation-of-the-epa-water-quality-improvement-grant-project-clean-watersheds-for-a-clean-bay/) - The Clean Watersheds for a Clean Bay (CW4CB) project was a collaboration among the Bay Area Stormwater Management Agencies Association (BASMAA) member agencies and the USEPA designed to evaluate the effectiveness of structural and non-structural controls to assist stormwater managers in meeting pollutant reduction targets.
- [Status and Trends Monitoring for the Regional Monitoring Program for Water Quality in San Francisco Bay](https://amarine.com/projects/status-and-trends-monitoring-for-the-regional-monitoring-program-for-water-quality-in-san-francisco-bay/) - The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) is a long-term monitoring program established in the early 1990s that investigates long-term trends in contamination in multiple media throughout San Francisco Bay. AMS has supported monitoring efforts associated with collection of water quality, sediment quality, and biotic information since project initiation and
- [USACE Fish Entrainment and Water Quality Monitoring](https://amarine.com/projects/usace-fish-entrainment-and-water-quality-monitoring/) - AMS has conducted investigations for the US Army Corps of Engineers (USACE) to support fish entrainment and water quality monitoring during maintenance dredging operations and at dredged material placement sites (DMPS). This work has been coordinated with the USACE and addresses management questions of importance to the State Water Board.
- [Third-Party Environmental Mitigation Measure Compliance Monitoring for the California State Lands Commission](https://amarine.com/projects/third-party-environmental-mitigation-measure-compliance-monitoring-for-the-california-state-lands-commission/) - AMS provided third-party independent environmental mitigation monitoring assessments at four marine oil terminals operating in San Francisco Bay Area. The California State Lands Commission (CSLC) is required to enact a program that assesses operations of marine oil terminals (MOTs) are consistent with the adopted mitigation measures defined in the associated Environmental Impact Report (EIR). The
- [Vallejo Marine Terminal CEQA Analysis and Marine Resources Assessment](https://amarine.com/projects/vallejo-marine-terminal-ceqa-analysis-and-marine-resources-assessment/) - AMS assisted Dudek and other team members in assessing potential environmental effects of a marine terminal in accordance with CEQA. AMS prepared the marine biological resource and impact assessment for the CEQA analysis, and conducted a benthic infauna and intertidal community and habitat assessment of the site.
- [Industrial General Permit Monitoring](https://amarine.com/projects/industrial-general-permit-monitoring/) - AMS QISP-trained scientists take on a variety of roles to assist regulated facilities to develop and implement required monitoring efforts to best ensure consistency with IGP requirements.
- [NEPA Analysis of the Mobile Ocean Test Berth](https://amarine.com/projects/nepa-analysis-of-the-mobile-ocean-test-birth/) - AMS provided expertise in marine habitat, biota, and fisheries in assessing the potential impacts from a mobile ocean-testing berth operated by Oregon State University offshore Newport, Oregon for the Department of Energy. This floating facility will be used by wave energy conversion developers to test and improve the efficiency and operational capability of current and future ocean energy technology.
- [Program Coordination of the Clean Estuary Partnership](https://amarine.com/projects/program-coordination-of-the-clean-estuary-partnership/) - AMS provided overall scientific project design, program management, and program facilitation for this multi-million dollar, multi-year project that provided scientific information in support of development and implementation of Total Maximum Daily Loads (TMDLs) and other water quality attainment strategies for the San Francisco Bay-Delta and its tributaries..
- [On-call Support for the California Energy Commission](https://amarine.com/projects/on-call-support-for-the-california-energy-commission/) - AMS is a Supporting Member of Offshore Wind California; a consortium of engineers, environmental consultants, developers, and energy companies working together to facilitate the development of offshore wind in California. AMS is providing marine consulting services to the California Energy Commission to help guide responsible energy and infrastructure development to help California meet its future energy
- [Offshore Wind](https://amarine.com/projects/offshore-wind/) - AMS’ long-standing collaborations with agency and academic researchers allows us to demonstrate our capabilities to address a wide variety of potential environmental concerns specific to the offshore wind arena. AMS is supporting both developers and regulatory agencies in furthering their efforts in this burgeoning field.
- [Pesticide Monitoring for the Marin County Stormwater Pollution Prevention Program](https://amarine.com/projects/pesticide-monitoring-for-marin-county-stormwater-pollution-prevention-program/) - AMS implemented a pesticide monitoring program to assess impacts of pesticide usage upon Marin County waterways in support of the Total Maximum Daily Load (TMDL) for Diazinon and Pesticide Related Toxicity in the San Francisco Bay Region.
- [Modeling Pollutants of Concern in San Francisco Bay](https://amarine.com/projects/modeling-pollutants-of-concern-in-san-francisco-bay/) - AMS scientists support the Small Tributaries Loading Strategy in efforts to evaluate methods to optimize the sampling design for monitoring pollutant loads from small tributaries, with the goal of predicting future trends in San Francisco Bay.
- [Sacramento River Surveys](https://amarine.com/projects/sacramento-river-mercury-bioaccumulation-study/) - AMS provided on-call support to the Sacramento Regional County Sanitation District in their efforts to characterize the biomass and composition of primary producers and clam grazers along the Sacramento River and its tributaries.
- [Scientific Study Support for Exxon Valdez Oil Spill](https://amarine.com/projects/scientific-study-support-for-exxon-valdez-oil-spill/) - AMS was selected by the US and State of Alaska Joint Trustee Council to provide the Chief Scientist and Assistant Chief Scientist for the government’s investigations of natural resource damages from the Exxon Valdez oil spill in Prince William Sound, Alaska.
- [Outfall and Ocean Water Monitoring for the City of Fort Bragg](https://amarine.com/projects/outfall-and-ocean-water-monitoring-for-the-city-of-fort-bragg/) - Beginning in 2007 and repeated on an approximately five-year basis, AMS designed a monitoring program, including SCUBA-supported biological and water quality sampling, to document the City of Fort Bragg’s compliance of their ocean outfall with conditions of the California Ocean Plan.
- [Delta RMP Contaminants of Concern Pilot Study](https://amarine.com/projects/delta-rmp-contaminants-of-concern-pilot-study/) - AMS is supporting the Delta RMP Contaminants of Concern (CECs) pilot project in monitoring a variety of emerging contaminants in water, sediment, and biota, including analysis of compounds with historic uses as hormones, plasticizers, pharmaceuticals and personal care products (PPCPs), flame retardants, and non-stick coatings.
- [Carmel Microbial Source Tracking](https://amarine.com/projects/carmel-microbial-source-tracking/) - AMS is supporting the city of Carmel-by-the-Sea in investigating sources of contamination of the Carmel Bay Area of Special Biological Significance (ASBS). AMS has employed microbial source tracking techniques utilizing markers for human, canine, and avian sources, as well as sampling of dissolved and total trace metals in storm drains and sub-watersheds that drain to
- [Stormwater Monitoring in Areas of Special Biological Significance](https://amarine.com/projects/areas-of-special-biological-significance/) - AMS supported the Monterey Regional Water Pollution Control Agency in implementing a regional monitoring program for Areas of Special Biological Significance (ASBS) along the Central California coast, predominantly associated with the Monterey Bay National Marine Sanctuary.
- [Review of Historic Monitoring at Ocean Dumping Sites](https://amarine.com/projects/review-of-historic-monitoring-at-ocean-dumping-sites/) - AMS assisted EPA’S Ocean Dumping Management Program in evaluating past monitoring activities conducted at ocean dredged material disposal sites (ODMDS). AMS prepared a summary report and webinar on the performance of ODMDS against programmatic requirements based on findings from 20 case-studies.
- [Monterey Peninsula Water Supply Project](https://amarine.com/projects/monterey-peninsula-water-supply-project/) - AMS investigated the impact of brine discharge from a proposed desalination plant into the Monterey Bay National Marine Sanctuary by conducting oceanographic modeling of the bay. AMS also assessed marine biological impacts based on the outcome of the physical processes modeling of salinity.
- [Investigations into Causes of Mortality in Southern Sea Otters](https://amarine.com/projects/persistent-organic-pollutants-in-sea-otters/) - For this Proposition 13 Grant study, AMS assessed the link between organic pollutant concentrations and mortality due to infectious diseases, in the federally endangered southern sea otter population in Monterey Bay, California.
- [Biological Assessment of a Fiber Optic Cable Route](https://amarine.com/projects/biological-assessment-of-a-fiber-optic-cable-route/) - AMS scientists conducted an ROV based characterization of seafloor habitats and associated marine biota along a 14 km segment of a proposed, new fiber optic telecommunication cable linking Southeast Asia and the US.
- [Freshwater Creek Bioassessments](https://amarine.com/projects/freshwater-creek-bioassessments/) - AMS has been heavily involved in the design and implementation of freshwater creek bioassessments on behalf of public and private National Pollutant Discharge Elimination System (NPDES) permit holders.
- [Marine Habitat Analysis for Link21](https://amarine.com/projects/assessment-of-marine-habitat-for-bart-link21-program/) - AMS is providing marine habitat services to the environmental team to help identify constraints and opportunities associated with marine biological resources.
- [Longfin Smelt Monitoring](https://amarine.com/projects/richmond-harbor-longfin-smelt-monitoring/) - AMS implemented longfin smelt monitoring activities according to protocols approved by CDFW associated with navigational dredging operations conducted within North San Francisco Bay by the US Army Corps of Engineers.
- [American Academy of Underwater Sciences (AAUS) Organizational Member](https://amarine.com/projects/american-academy-of-underwater-sciences-aaus-organizational-member/) - MS is an American Academy of Underwater Sciences (AAUS) Organizational Member. The AAUS is an international consortium of universities, government agencies, museums, aquariums, environmental consulting firms, community science groups, and individuals that are committed to safety and using scuba diving for research.
- [Technical Support for the Alameda Countywide Clean Water Program](https://amarine.com/projects/technical-support-for-the-alameda-countywide-clean-water-program-2/) - The Alameda Countywide Clean Water Program (ACCWP) is the NPDES stormwater permit holder for Alameda County. AMS has supported the ACCWP in achieving compliance with its respective stormwater NPDES permits by conducting a variety of scientific and engineering investigations addressing various management questions of interest to collaborating municipalities and regulatory agencies.
- [Mitigation Monitoring of the Chevron Long Wharf](https://amarine.com/projects/chevron-marine-oil-terminal-monitoring/) - AMS designed a multi-year compliance monitoring program and managed its implementation for the California State Lands Commission at the Chevron Long Wharf in Richmond, CA.
- [Compliance Monitoring for Hermosa Beach Fiber Optic Cable Landing](https://amarine.com/projects/compliance-monitoring-for-hermosa-beach-fiber-optic-cable-landing/) - AMS scientists were responsible for monitoring four Horizontal Directionally Drilled (HDD) bore holes in Hermosa Beach, California. A key component of this permit compliance validation effort was the monitoring of the HDD drilling operations for potential drilling fluid releases both onshore and offshore along each bores trajectory.
- [San Francisco Pier 70 CEQA Analysis](https://amarine.com/projects/san-francisco-pier-70-ceqa-analysis/) - AMS characterized and defined the existing marine biological communities and habitats for the Port of San Francisco’s Pier 70 redevelopment project in accordance with California Environment Quality Act (CEQA).
- [Coastal Desalination](https://amarine.com/projects/coastal-desalination/) - AMS has been the lead marine resources contractor on multiple desalination projects in California, including the West Basin Desal project and the Interagency Desal project. AMS has prepared the marine resources section of the Environmental Impact Report for each project, evaluating potential impacts and recommending measures to avoid negative effects. Special studies were also conducted to assess plankton communities and potential entrainment.
- [CEQA / NEPA Analysis for the 34th America’s Cup Races](https://amarine.com/projects/port-of-san-francisco-americas-cup-races-ceqa-nepa/) - In support of the most recent America’s Cup Races in San Francisco Bay, AMS prepared the marine-related components of required CEQA and NEPA documentation for involved parties, including City/County of San Francisco, the National Park Service, US Coast Guard and US Army Corps of Engineers, National Marine Fisheries Service, and the California Department of Fish
- [Mitigation Monitoring for Fiberoptic Cable Installations at Grover Beach](https://amarine.com/projects/mitigation-monitoring-for-fiberoptic-cable-installations-at-grover-beach/) - In support of installation of four submarine cables, AMS scientists conducted site assessments of potential submerged aquatic vegetation beds in the HDD bore offshore terminus locations using SCUBA, and also performed compliance monitoring in onshore and offshore locations during drilling operations on behalf of the California State Lands Commission.
- [Steelhead Restoration in Alameda Creek Watershed](https://amarine.com/projects/steelhead-restoration-in-alameda-creek-watershed/) - AMS provided technical and administrative support to a workgroup investigating the feasibility of restoring a historic steelhead run to Alameda Creek, the largest local watershed draining to San Francisco Bay. Based upon these early efforts, the Workgroup was able to secure funding to support multi-million dollar restoration efforts within the watershed.
- [Mitigation Monitoring of Marine Oil Terminals for California State Lands Commission](https://amarine.com/projects/mitigation-monitoring-of-marine-oil-terminals-for-california-state-lands-commission/) - Under contract to the State of California, AMS provided third-party independent environmental mitigation monitoring of multiple San Francisco Bay Area Marine Oil Terminals. AMS, as the lead of a multidisciplinary team of scientists and engineers, assessed each marine terminal operator’s compliance with environmental mitigation measures and lease requirements implemented as part of their respective 30-year lease renewals from the California State Lands Commission. This multi-year
- [Eureka Fiber Optic Cable Installation](https://amarine.com/projects/eureka-fiber-optic-cable-installation/) - AMS was instrumental in the planning and preliminary work for three trans-Pacific fiberoptic cable landings into Eureka, California; two of these cables run through the proposed Humboldt Wind Energy Area (WEA).
- [Central Coast Long-Term Environmental Assessment Network (CCLEAN)](https://amarine.com/projects/central-coast-long-term-environmental-assessment-network-cclean/) - AMS led the effort to design the Central Coast Long-term Environmental Assessment Network (CCLEAN) regional monitoring program and provides ongoing technical direction and management. This program is funded by four municipal dischargers and an industrial discharger, under direction from the State of California Central Coast Regional Water Quality Control Board. Based upon a consensus-building approach, the program
- [Monitoring of Stockton and Sacramento Deep Water Ship Channels](https://amarine.com/projects/monitoring-of-stockton-and-sacramento-deep-water-ship-channels/) - Following several previous investigations for the US Army Corps of Engineers (USACE), AMS has been conducting monitoring of methylmercury (MeHg) in the Stockton and Sacramento Deep Water Ship Channels during maintenance dredging operations and in dredged material placement sites. AMS’ responsibilities includes coordination of all field activities, subcontracting for analytical services, data management and quality
- [San Francisco Bay Regional Monitoring Program](https://amarine.com/projects/san-francisco-bay-regional-monitoring-program/) - AMS is instrumental in the design and management of this multi-million dollar annual program for the San Francisco Estuary Institute (SFEI) and the San Francisco Regional Water Quality Control Board. The program samples water and sediments for trace elements, trace organic chemicals, and toxicity. It also includes a bioaccumulation monitoring element in which transplanted mussels
- [Clean Watersheds for a Clean Bay](https://amarine.com/projects/clean-watersheds-for-a-clean-bay/) - AMS provided support to Bay Area Stormwater Management Agencies Association for the implementation of an Environmental Protection Agency Water Quality Improvement Fund grant to assist stormwater management agencies in meeting Total Maximum Daily Load (TMDL) pollutant reduction targets. AMS participated in project management team activities, oversaw quality assurance and monitoring efforts, and provided data management
- [Mercury TMDL Allocations and Implementation Scheme for San Francisco Bay](https://amarine.com/projects/mercury-tmdl-allocations-and-implementation-scheme-for-san-francisco-bay/) - AMS prepared technical reports documenting mercury loads to San Francisco Bay from wastewater, wetlands, atmospheric deposition, toxic clean-up sites, and abandoned mercury mines. AMS managed the work of several contractors, and results from this work were used by the Water Board for the development of mercury Total Maximum Daily Load for the San Francisco Estuary.
- [Technical Support for the Alameda Countywide Clean Water Program](https://amarine.com/projects/technical-support-for-the-alameda-countywide-clean-water-program/) - AMS provides technical assistance to the Alameda Countywide Clean Water Program in support of the program’s National Pollutant Discharge Elimination System (NPDES) permit. Our scientists provide the program with monitoring, analysis, and reporting consistent with the municipal regional stormwater permit requirements. In addition, AMS reviews literature of various pollutants of concern to stormwater managers, performs
- [Monitoring of Combined Stormwater and Sewer Discharge](https://amarine.com/projects/monitoring-of-combined-stormwater-and-sewer-discharge/) - AMS is supporting the San Francisco Public Utilities Commission (SFPUC) in developing a Receiving Water Model as part of its Sewer System Improvement Program (SSIP), by assisting with project scoping and developing a Sampling and Analysis Plan (SAP) to implement monitoring of combined stormwater and sewer discharge events, both at the outfall and in nearshore
- [San Francisco Nearshore Current Measurements](https://amarine.com/projects/san-francisco-nearshore-currents-measurements/) - The San Francisco Public Utilities Commission Wastewater Enterprise is in the process of developing a receiving water model as part of it sewer system improvement program. AMS deploys current profiling instruments, completes data analysis, and incorporates climate data to provide quantified information for numerical modeling. AMS staff is also providing input to the modelers to
- [Mitigation Monitoring Program for San Francisco Bay Marine Oil Terminals](https://amarine.com/projects/mitigation-monitoring-program-for-san-francisco-bay-marine-oil-terminals/) - AMS was awarded a multi-year contract by the California State Lands Commission (CSLC) to oversee implementation of the mitigation monitoring program at the Chevron Long Wharf in Richmond, CA. AMS designed the overall approach and process for assessing annual compliance with the required mitigation measures and other permit requirements issued as part of the State
- [Monitoring Pollutant Removal Efficiencies of Urban Structural Retrofits for the EPA Water Quality Improvement Fund Grant, Clean Watersheds For a Clean Bay](https://amarine.com/projects/monitoring-pollutant-removal-efficiencies-of-urban-structural-retrofits-for-the-epa-water-quality-improvement-fund-grant-clean-watersheds-for-a-clean-bay/) - AMS provided on-call support to the Bay Area Stormwater Management Agencies Association in implementation.
- [Native Oysters at San Leandro Marina](https://amarine.com/projects/native-oysters-at-san-leandro-marina/) - AMS scientists conducted assessments of native oysters within and adjacent to the San Leandro Marina to characterize their relative abundances, distributions, and survival rates on docks and pier pilings, as well as in the intertidal zone. Our investigation evaluated potential environmental stresses affecting oyster recruitment and growth, and potential effects that planned marine improvements would
- [The “Bad Suisun” Phenomenon](https://amarine.com/projects/the-bad-suisun-phenomenon/) - AMS and co-PI University of California at Santa Cruz investigated whether elevated levels of ammonium can be related to phytoplankton physiological stress in Suisun Bay using active fluorometry. In addition, levels of ammonium needed to cause a decline in primary production in individual phytoplankton was characterized under controlled conditions. This project will have ramifications for
- [Sacramento River Surveys](https://amarine.com/projects/sacramento-river-surveys/) - AMS provides on-call support to the Sacramento Regional County Sanitation District in their efforts to characterize the biomass and composition of primary producers and their grazers along the Sacramento River and its tributaries.
- [Clam – Effluent Bioassays](https://amarine.com/projects/clam-effluent-bioassays/) - AMS provided technical support to the Sacramento Regional County Sanitation District in researching scientific questions related to effluent discharge into the Sacramento River.
- [Kashagan Oil and Gas Field Environmental Review](https://amarine.com/projects/kashagan-oil-and-gas-field-environmental-review/) - AMS, in conjunction with its subcontractors, Mariposa Environmental and Reese-Chambers Systems Consultants, provided expert environmental impact review and assessment support to AGIP-KCO in their development of the Kashagan Field oil and gas Experimental Program in the North Caspian Sea region of Kazakhstan. The project team, headed by AMS, reviewed all environmental impact assessment documents prepared
- [Pacific Outer Continental Shelf Oil & Gas Operations Monitoring for the US Department of the Interior](https://amarine.com/projects/pacific-outer-continental-shelf-oil-gas-operations-monitoring-for-the-us-department-of-the-interior/) - AMS was selected by the Department of the Interior (DOI) Bureau of Ocean Energy Management (BOEM) to provide on-call scientific monitoring of all Outer Continental Shelf (OCS) oil and gas operations in the Pacific Region as a key part of their environmental mitigation monitoring program. This 5-year project involved AMS implementing scientific studies to evaluate the effectiveness of environmental
- [Fiber Optic Cable Installation](https://amarine.com/projects/fiber-optic-cable-installation/) - AMS has been instrumental in the siting, permitting and installation of trans-Pacific fiber optic cable landings into California since 1999. AMS has prepared marine habitat and resources documents in support of CEQA assessments, conducted SCUBA diver and Remotely Operated Vehicle (ROV) surveys of cable corridors for sensitive habitats and species, monitored for the State of California the Horizontally Directionally Drilled Cable (HDD)
- [Mapping of Ammonium Concentrations in Suisun Bay and Sacramento River](https://amarine.com/projects/mapping-of-ammonium-concentrations-in-suisun-bay-and-sacramento-river/) - Data, such as high-resolution ammonium concentrations, can be used to create snap-shots over large spatial scales as this image of Suisun Bay and the Sacramento River.
- [Ammonium Dose-Reponse Experiment](https://amarine.com/projects/ammonium-dose-reponse-experiment/) - AMS and co-PI University of California at Santa Cruz performed dose-response experiments to test the effects of elevated levels of ammonium on phytoplankton isolated from Suisun Bay. Varying concentrations of ammonium were added to pure cultures and phytoplankton were incubated under controlled conditions for seven days. Subsamples for active fluorometry, cell counts, nutrients, and chl-a
- [Characterizing Intertidal Assemblages](https://amarine.com/projects/characterizing-intertidal-assemblages/) - AMS scientists designed and implemented a program to assess intertidal assemblages and evaluate concentrations of petroleum hydrocarbons at the Point Reyes National Seashore for the National Park Service (NPS). The objective of the program was to describe baseline conditions for Natural Resource Damage Assessment (NRDA) actions that may be necessary in the event of a

## Documents

- [Intertidal Habitat and Marine Biota Survey of the Vallejo Marine Terminal Site, Vallejo, California](https://amarine.com/documents/intertidal-habitat-and-marine-biota-survey-of-the-vallejo-marine-terminal-site-vallejo-california/)
- [Central Coast Regional Monitoring Program - Water Quality in Areas of Special Biological Significance: Final Report 2013-2016](https://amarine.com/documents/central-coast-regional-monitoring-program-water-quality-in-areas-of-special-biological-significance-final-report-2013-2016/)
- [Factors influencing methylmercury contamination of black bass from California reservoirs](https://amarine.com/documents/factors-influencing-methylmercury-contamination-of-black-bass-from-california-reservoirs/) - Abstract Understanding how mercury (Hg) accumulates in the aquatic food web requires information on the factors driving methylmercury (MeHg) contamination. This paper employs data on MeHg in muscle tissue of three black bass species (Largemouth Bass, Spotted Bass, and Smallmouth Bass) sampled from 21 reservoirs in California. During a two-year period, reservoirs were sampled for
- [Sacramento River Deep Water Ship Channel Deepening Project: Methylmercury Production in Dredged Material Placement Areas II](https://amarine.com/documents/sacramento-river-deep-water-ship-channel-deepening-project-methylmercury-production-in-dredged-material-placement-areas-ii/)
- [Investigation of Best Management Practices to Limit Loadings of Methyl Mercury Associated with Planned Dredging Activities in Sacramento and San Joaquin River Deep Water Ship Channels](https://amarine.com/documents/investigation-of-best-management-practices-to-limit-loadings-of-methyl-mercury-associated-with-planned-dredging-activities-in-sacramento-and-san-joaquin-river-deep-water-ship-channels/)
- [Distribution and Trends of Select Marine Debris Items Collected During International Coastal Cleanup (ICC) Events, 2001-2010](https://amarine.com/documents/distribution-and-trends-of-select-marine-debris-items-collected-during-international-coastal-cleanup-icc-events-2001-2010/)
- [Central Coast Long-term Environmental Assessment Network - Regional Monitoring Program: Annual Report 2015-16](https://amarine.com/documents/central-coast-long-term-environmental-assessment-network-regional-monitoring-program-annual-report-2015-16/)
- [Monitoring and Mitigation to Address Fecal Pathogen Pollution along California Coast](https://amarine.com/documents/monitoring-and-mitigation-to-address-fecal-pathogen-pollution-along-california-coast/)
- [Benthic Survey of Commercial Aggregate Mining Leases in Central San Francisco Bay and Western Delta](https://amarine.com/documents/benthic-survey-of-commercial-aggregate-mining-leases-in-central-san-francisco-bay-and-western-delta/)
- [Assessment and Evaluation of Fish and Invertebrate Entrainment Effects from Commercial Aggregate Sand Mining in San Francisco Estuary](https://amarine.com/documents/assessment-and-evaluation-of-fish-and-invertebrate-entrainment-effects-from-commercial-aggregate-sand-mining-in-san-francisco-estuary/)
- [Benthic Survey of Proposed Treasure Island, California Redevelopment Ferry Terminal Location](https://amarine.com/documents/benthic-survey-of-proposed-treasure-island-california-redevelopment-ferry-terminal-location/)
- [Intertidal Habitat and Marine Biota Survey of Treasure Island and the West Side of Yerba Buena Island, California](https://amarine.com/documents/intertidal-habitat-and-marine-biota-survey-of-treasure-island-and-the-west-side-of-yerba-buena-island-california/)
- [Remotely Operated Vehicle (ROV) Biological Characterization Survey of the Asia America Gateway (AAG) S-5 Project Fiber Optic Cable Route Offshore Morro Bay, California](https://amarine.com/documents/remotely-operated-vehicle-rov-biological-characterization-survey-of-the-asia-america-gateway-aag-s-5-project-fiber-optic-cable-route-offshore-morro-bay-california/)
- [Benthic Survey Of The Vallejo Marine Terminal LLC Site Vallejo, California](https://amarine.com/documents/benthic-survey-of-the-vallejo-marine-terminal-llc-site-vallejo-california/)
- [Seafloor Habitat & Biological Characterization Assessment of the SEA-US Fiber Optic Cable Route Offshore Hermosa Beach, California by Remotely Operated Vehicle (ROV)](https://amarine.com/documents/seafloor-habitat-biological-characterization-assessment-of-the-sea-us-fiber-optic-cable-route-offshore-hermosa-beach-california-by-remotely-operated-vehicle-rov/)
- [Subtidal Habitats and Associated Macrobenthic and Fish Communities Observed Offshore Coastal California Along Fiber Optic Cable Routes](https://amarine.com/documents/subtidal-habitats-associated-macrobenthic-fish-communities-observed-offshore-coastal-california-along-fiber-optic-cable-routes/)
- [Methylmercury Best Management Practice Evaluation, 2011 Sacramento and Stockton Deep Water Shipping Channel Maintenance Dredging Project](https://amarine.com/documents/methylmercury-best-management-practice-evaluation-2011-sacramento-and-stockton-deep-water-shipping-channel-maintenance-dredging-project/)
- [A tiered assessment framework to evaluate human health risk of contaminated sediment](https://amarine.com/documents/a-tiered-assessment-framework-to-evaluate-human-health-risk-of-contaminated-sediment/)
- [Seasonal and annual trends in forage fish mercury concentrations](https://amarine.com/documents/seasonal-and-annual-trends-in-forage-fish-mercury-concentrations/)
- [Estimated Sediment Contaminant Concentrations Associated with Biological Impacts at San Diego Bay Clean-up Sites](https://amarine.com/documents/estimated-sediment-contaminant-concentrations-associated-with-biological-impacts-at-san-diego-bay-clean-up-sites/)
- [Optimizing sampling methods for pollutant loads and trends in San Francisco Bay urban stormwater monitoring. A technical report for the Sources Pathways and Loading Workgroup of the Regional Monitoring Program for Water Quality.](https://amarine.com/documents/optimizing-sampling-methods-for-pollutant-loads-and-trends-in-san-francisco-bay-urban-stormwater-monitoring-a-technical-report-for-the-sources-pathways-and-loading-workgroup-of-the-regional-monitorin/)
- [Conceptual Foundations for Modeling Bioaccumulation in San Francisco Bay.](https://amarine.com/documents/conceptual-foundations-for-modeling-bioaccumulation-in-san-francisco-bay/)
- [Spatial trends and impairment assessment of mercury in fish from the Sacramento-San Joaquin Delta watershed.](https://amarine.com/documents/spatial-trends-and-impairment-assessment-of-mercury-in-fish-from-the-sacramento-san-joaquin-delta-watershed/)
- [Mussel Watch Update: Long-term trends in selected contaminants from coastal California, 1977- 2010](https://amarine.com/documents/mussel-watch-update-long-term-trends-in-selected-contaminants-from-coastal-california-1977-2010/)
- [Benthic macrofaunal assemblages of the San Francisco Estuary and Delta, USA](https://amarine.com/documents/benthic-macrofaunal-assemblages-of-the-san-francisco-estuary-and-delta-usa/)
- [The slow recovery of San Francisco Bay from the legacy of organochlorine pesticides.](https://amarine.com/documents/the-slow-recovery-of-san-francisco-bay-from-the-legacy-of-organochlorine-pesticides/)
- [Spatial Variation in Hard-Bottom Epifauna in the Santa Maria Basin, California: The Importance of Physical Factors. ](https://amarine.com/documents/spatial-variation-in-hard-bottom-epifauna-in-the-santa-maria-basin-california-the-importance-of-physical-factors/)
- [A Biological and Physical Monitoring Program to Evaluate Long-term Impacts from San Dredging Operations in the United States Outer Continental Shelf.](https://amarine.com/documents/a-biological-and-physical-monitoring-program-to-evaluate-long-term-impacts-from-san-dredging-operations-in-the-united-states-outer-continental-shelf/)
- [Evidence for a novel marine harmful algal bloom: cyanotoxin (microcystin) transfer from land to sea otters.](https://amarine.com/documents/evidence-for-a-novel-marine-harmful-algal-bloom-cyanotoxin-microcystin-transfer-from-land-to-sea-otters/)
- [Variation in Growth Rate, Carbon Assimilation, and Photosynthetic Efficiency in Response to Nitrogen Source and Concentration in Phytoplankton Isolated from Upper San Francisco Bay.](https://amarine.com/documents/variation-in-growth-rate-carbon-assimilation-and-photosynthetic-efficiency-in-response-to-nitrogen-source-and-concentration-in-phytoplankton-isolated-from-upper-san-francisco-bay/)
- [Monitoring long-term effects of offshore oil and gas development along the southern California outer continental shelf and slope: Background environmental conditions in the Santa Maria Basin.](https://amarine.com/documents/monitoring-long-term-effects-of-offshore-oil-and-gas-development-along-the-southern-california-outer-continental-shelf-and-slope-background-environmental-conditions-in-the-santa-maria-basin/)
- [The Regional Monitoring Program for Water Quality in San Francisco Bay, California, USA: Science in support of managing water quality.](https://amarine.com/documents/the-regional-monitoring-program-for-water-quality-in-san-francisco-bay-california-usa-science-in-support-of-managing-water-quality/)
- [Variation in particulate C and N isotope composition following iron fertilization in two successive phytoplankton communities in the Southern Ocean](https://amarine.com/documents/variation-in-particulate-c-and-n-isotope-composition-following-iron-fertilization-in-two-successive-phytoplankton-communities-in-the-southern-ocean/)
- [The role of the picoeukaryote Aureococcus anophagefferens in cycling of marine high-molecular weight dissolved organic nitrogen.](https://amarine.com/documents/the-role-of-the-picoeukaryote-aureococcus-anophagefferens-in-cycling-of-marine-high-molecular-weight-dissolved-organic-nitrogen/)
- [Plankton community composition in relation to availability and uptake of oxidized and reduced nitrogen](https://amarine.com/documents/plankton-community-composition-in-relation-to-availability-and-uptake-of-oxidized-and-reduced-nitrogen/)
- [Responses of hli, ptox and psbA genes to changes in irradiance in marine Synechococcus and Prochlorococcus](https://amarine.com/documents/responses-of-hli-ptox-and-psba-genes-to-changes-in-irradiance-in-marine-synechococcus-and-prochlorococcus/)
- [Factors affecting the growth of cyanobacteria with special emphasis on the Sacramento-San Joaquin Delta](https://amarine.com/documents/factors-affecting-the-growth-of-cyanobacteria-with-special-emphasis-on-the-sacramento-san-joaquin-delta/)
- [Impact of atypical ammonium concentrations on phytoplankton abundance and composition in fresh versus estuarine waters](https://amarine.com/documents/impact-of-atypical-ammonium-concentrations-on-phytoplankton-abundance-and-composition-in-fresh-versus-estuarine-waters/)
- [Strategies and rates of photoacclimation in two major Southern Ocean phytoplankton taxa: Phaeocystis antarctica (Haptophyta) and Fragilariopsis cylindrus (Bacillariophyceae)](https://amarine.com/documents/strategies-and-rates-of-photoacclimation-in-two-major-southern-ocean-phytoplankton-taxa-phaeocystis-antarctica-haptophyta-and-fragilariopsis-cylindrus-bacillariophyceae/)
- [Photophysiology in two major Southern Ocean phytoplankton taxa: Photosynthesis of Phaeocystis antarctica (Prymnesiophyceae) and Fragilariopsis cylindrus (Bacillariophyceae) under simulated mixed layer irradiance](https://amarine.com/documents/photophysiology-in-two-major-southern-ocean-phytoplankton-taxa-photosynthesis-of-phaeocystis-antarctica-prymnesiophyceae-and-fragilariopsis-cylindrus-bacillariophyceae-under-simulated-mixed-layer/)
- [Role of urea in microbe metabolism in aquatic systems: a biochemical and molecular review](https://amarine.com/documents/role-of-urea-in-microbe-metabolism-in-aquatic-systems-a-biochemical-and-molecular-review/)
- [Porphyra: complex life histories in a harsh environment](https://amarine.com/documents/porphyra-complex-life-histories-in-a-harsh-environment/)
- [Deep carbon export from a Southern Ocean iron-fertilized diatom bloom](https://amarine.com/documents/deep-carbon-export-from-a-southern-ocean-iron-fertilized-diatom-bloom/)
- [Analysis of Porphyra membrane transporters demonstrates gene transfer among photosynthetic eukaryotes and numerous sodium-coupled transport systems](https://amarine.com/documents/analysis-of-porphyra-membrane-transporters-demonstrates-gene-transfer-among-photosynthetic-eukaryotes-and-numerous-sodium-coupled-transport-systems/)
- [Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics](https://amarine.com/documents/niche-of-harmful-alga-aureococcus-anophagefferens-revealed-through-ecogenomics/)
- [Suisun Bay Ammonium Synthesis Report](https://amarine.com/documents/suisun-bay-ammonium-synthesis-report/)
- [Determining the Potential Release of Contaminants into the Marine Environment from Pacific OCS Shell Mounds](https://amarine.com/documents/determining-the-potential-release-of-contaminants-into-the-marine-environment-from-pacific-ocs-shell-mounds/)
- [Power Analysis and Optimization of the RMP Status and Trends Program](https://amarine.com/documents/power-analysis-and-optimization-of-the-rmp-status-and-trends-program/)
- [PCBs in Urban Watersheds—A Challenge for TMDL Implementation](https://amarine.com/documents/pcbs-in-urban-watersheds-a-challenge-for-tmdl-implementation/)
- [Municipal Maintenance and Sediment Management: Evaluation of Source Control Options for TMDL Implementation](https://amarine.com/documents/municipal-maintenance-and-sediment-management-evaluation-of-source-control-options-for-tmdl-implementation/)
- [2000-01 Alameda County Watershed Sediment Sampling Program: Two-Year Summary and Analysis](https://amarine.com/documents/2000-01-alameda-county-watershed-sediment-sampling-program-two-year-summary-and-analysis/)
- [Persistent Organic Pollutant Concentrations in Southern Sea Otters (Enhydra lutris nereis): Patterns With Respect To Environmental Risk Factors and Major Causes Of Mortality](https://amarine.com/documents/persistent-organic-pollutant-concentrations-in-southern-sea-otters-enhydra-lutris-nereis-patterns-with-respect-to-environmental-risk-factors-and-major-causes-of-mortality/)
- [2011 Longfin Smelt Monitoring During Dredging By The USACE Hopper Dredge Essayons In The San Francisco Bay Area](https://amarine.com/documents/2011-longfin-smelt-monitoring-during-dredging-by-the-usace-hopper-dredge-essayons-in-the-san-francisco-bay-area/)
- [Novel analyses of long-term data provide a scientific basis for chlorophyll-a thresholds in San Francisco Bay](https://amarine.com/documents/novel-analyses-of-long-term-data-provide-a-scientific-basis-for-chlorophyll-a-thresholds-in-san-francisco-bay/)
- [Statistical Methods Development and Sampling Design Optimization to Support Trends Analysis for Loads of Polychlorinated Biphenyls from the Guadalupe River in San Jose, California, USA, Final Report](https://amarine.com/documents/statistical-methods-development-and-sampling-design-optimization-to-support-trends-analysis-for-loads-of-polychlorinated-biphenyls-from-the-guadalupe-river-in-san-jose-california-usa-final-report/)
- [Effects of nitrogen source, concentration, and irradiance on growth rates of two diatoms endemic to northern San Francisco Bay](https://amarine.com/documents/effects-of-nitrogen-source-concentration-and-irradiance-on-growth-rates-of-two-diatoms-endemic-to-northern-san-francisco-bay/)

## Categories

- [Uncategorized](https://amarine.com/category/uncategorized/)

## Tags

- [Biological Studies](https://amarine.com/tag/biological-studies/)
- [Methylmercury](https://amarine.com/tag/methylmercury/)
- [Data/Geospatial Analyses](https://amarine.com/tag/data-geospatial-analyses/)
- [Ammonia Toxicity](https://amarine.com/tag/ammonia-toxicity/)
- [Ammonium](https://amarine.com/tag/ammonium/)
- [Nitrogen Biochemistry](https://amarine.com/tag/nitrogen-biochemistry/)
- [Phytoplankton](https://amarine.com/tag/phytoplankton/)
- [Primary Production](https://amarine.com/tag/primary-production/)
- [Nutrients](https://amarine.com/tag/nutrients/)
- [Stakeholder Relations](https://amarine.com/tag/stakeholder/)
- [Water Quality Objectives](https://amarine.com/tag/water-quality/)
- [Beneficial Uses](https://amarine.com/tag/beneficial-uses/)
- [Sampling Design](https://amarine.com/tag/sampling-design/)
- [Statistical Analysis](https://amarine.com/tag/statistical-analysis/)
- [Stormwater Management](https://amarine.com/tag/stormwater-management/)
- [TMDL Support](https://amarine.com/tag/tmdl-support/)
- [Hard-bottom Subtidal](https://amarine.com/tag/hard-bottom-subtidal/)
- [ROV Survey](https://amarine.com/tag/rov-survey/)
- [Fisheries Assessments](https://amarine.com/tag/fisheries-assessments/)
- [Eutrophication and Algal Bloom Assessments](https://amarine.com/tag/eutrophication-and-algal-bloom-assessments/)
- [Fiber Optic Cables](https://amarine.com/tag/fiber-optic-cables/)
- [Benthic Infauna/Epifauna](https://amarine.com/tag/benthic-infauna-epifauna/)
- [Dredging](https://amarine.com/tag/dredging/)
- [Marine Terminals](https://amarine.com/tag/marine-terminals/)
- [Intertidal](https://amarine.com/tag/intertidal/)
- [Benthic Community Impacts](https://amarine.com/tag/benthic-community-impacts/)
- [Entrainment](https://amarine.com/tag/entrainment/)
- [Longfin Smelt](https://amarine.com/tag/longfin-smelt/)
- [Pathogens](https://amarine.com/tag/pathogens/)
- [Surface Water Quality](https://amarine.com/tag/surface-water-quality/)
- [Endocrine Disruptors](https://amarine.com/tag/endocrine-disruptors/)
- [Pesticides](https://amarine.com/tag/pesticides/)
- [Contaminant](https://amarine.com/tag/contaminant/)
- [Peer Review](https://amarine.com/tag/peer-review/)
- [Sources Pathways and Loads](https://amarine.com/tag/sources-pathways-and-loads/)
- [Best Management Practices](https://amarine.com/tag/best-management-practices/)
- [Load Reductions](https://amarine.com/tag/load-reductions/)
- [Consensus Building](https://amarine.com/tag/consensus-building/)
- [Urban Creeks](https://amarine.com/tag/urban-creeks/)
- [Receiving Water](https://amarine.com/tag/receiving-water/)
- [Water Quality Monitoring](https://amarine.com/tag/water-quality-monitoring/)
- [Regulatory Agency Interactions](https://amarine.com/tag/regulatory-agency-interactions/)
- [Oil and Gas](https://amarine.com/tag/oil-and-gas/)
- [Harmful Algal Blooms (HABs)](https://amarine.com/tag/harmful-algal-blooms-habs/)
- [Macroalgae](https://amarine.com/tag/macroalgae/)
- [Cyanotoxins](https://amarine.com/tag/cyanotoxins/)
- [Collaborative Design](https://amarine.com/tag/collaborative-design/)
- [Contaminant Effect Studies](https://amarine.com/tag/contaminant-effect-studies/)
- [Impairments](https://amarine.com/tag/impairments/)
- [Sediment transport](https://amarine.com/tag/sediment-transport/)
- [Hydrocarbons](https://amarine.com/tag/hydrocarbons/)
- [RCM1](https://amarine.com/tag/rcm1/)
- [EI1](https://amarine.com/tag/ei1/)
- [EA1](https://amarine.com/tag/ea1/)
- [EPM1](https://amarine.com/tag/epm1/)
- [EA2](https://amarine.com/tag/ea2/)
- [EI2](https://amarine.com/tag/ei2/)
- [EPM2](https://amarine.com/tag/epm2/)
- [RCM2](https://amarine.com/tag/rcm2/)
- [WQM2](https://amarine.com/tag/wqm2/)
- [WQM1](https://amarine.com/tag/wqm1/)
- [Featured](https://amarine.com/tag/featured/)