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Werme, C. 2012. Estuary News RMP Insert 2012. Estuary News. San Francisco Estuary Institute: Richmond, CA.
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Meadows, R. 2013. Estuary News RMP Insert 2013. Estuary News. San Francisco Estuary Institute: Richmond, CA.
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David, N.; Greenfield, B. K.; Siemering, G. S. 2006. Evaluating impacts of Lake Maid plant control. Journal of Aquatic Plant Management 44, 60-66.
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Greenfield, B. K.; Siemering, G.; David, N. 2005. Evaluating impacts of Lake Sweeper plant control. J. of Aquatic Plant Management . SFEI Contribution No. 461.
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Gunther, A. J.; Davis, J. A. 1998. An evaluation of bioaccumulation monitoring with transplanted bivalves in the RMP. SFEI Contribution No. 322. San Francisco Estuary Institute: Richmond, CA. pp 187-200.
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Yee, D.; Wong, A. 2019. Evaluation of PCB Concentrations, Masses, and Movement from Dredged Areas in San Francisco Bay. SFEI Contribution No. 938. San Francisco Estuary Institute: Richmond, CA.
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O'Connor, J. M. 1991. Evaluation of Turbidity and Turbidity Related Effects on the Biota of the San Francisco Bay-Delta Estuary. SFEI Contribution No. 169. San Francisco Estuary Institute: Richmond, CA. p 84.
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Collins, J. N. 2002. Executive Summary 2002 (Wetlands Science Program). SFEI Contribution No. 250. San Francisco Estuary Institute. p 4.
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Phillips, A. 1988. Executive Summary of the Monitoring of Toxic Contaminants in the San Francisco Bay-Delta: A Crtical Review. SFEI Contribution No. 151. San Francisco Estuary Institue: Richmond, CA. p 14.
Phillips, D. J. H. 1987. Executive Summary of Toxic Contaminats in the San Francisco Bay - Delta and Their Possible Biological Effects. SFEI Contribution No. 139. San Francisco Estuary Institute: Richmond, CA. p 15.
Collins, J. N. 2002. Executive Summary: SFEI Component of the Integrated Regional Wetlands Monitoring Pilot Project. SFEI Contribution No. 251. San Francisco Estuary Institute. p 2.
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Cohen, A. N. 1998. Exotic organisms; California's Emerging Environmental Challenges. California's Emerging Environmental Challenges; Proceedings of a Workshop, 5-9 to 5-13.
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Cohen, A. N. 2002. Exotic organisms in southern California Bays and Harbors. Marine Bioinvasions Conference . SFEI Contribution No. 481.
Cohen, A. N.; Lambert, C. C.; Harris, L. H.; Chapman, J. W.; Schwindt, E.; Reardon, K.; Rao, L. C.; Murray, S. N.; Ljubenkov, J. C.; Lambert, G.; et al. 2003. Exotic Organisms in Southern California Bays and Harbors. Page 22 in:. In Abstracts, Third International Conf. on Marine Bioinvasions, Mar. 16-19, Scripps Institution of Oceanography, La Jolla, CA. Abstracts, Third International Conf. on Marine Bioinvasions, Mar. 16-19, Scripps Institution of Oceanography, La Jolla, CA. p p. 22.
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Cohen, A. N. 2004. An Exotic Species Detection Program for Puget Sound. SFEI Contribution No. 380. San Francisco Estuary Institute: Oakland.
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Cohen, A. N. 2004. An Exotic Species Detection Program for the Lower Columbia River Estuary. SFEI Contribution No. 381. San Francisco Estuary Institute: Oakland.
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Cohen, A. N. 2004. An Exotic Species Detection Program for Tillamook Bay. SFEI Contribution No. 379. San Francisco Estuary Institute: Oakland.
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Cohen, A. N. 1998. Exotic species in California's coastal waters. Sanctuary Currents '98, Symposium on the Monterey Bay National Marine Sanctuary.
Cohen, A. N. 1998. The exotic species threat to California's coastal resources. SFEI Contribution No. 386. American Society of Civil Engineers: Reston, VA. pp 1418-1426.
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Cohen, A. N. 1998. The exotic species threat to California's coastal resources. California and the World Ocean '97, 1418-1426.
Foley, M.; Christian, E.; Goeden, B.; Ross, B. 2020. Expert review of the sediment screening guidelines for the beneficial reuse of dredged material in San Francisco Bay. SFEI Contribution No. 978. San Francisco Estuary Institute: Richmond, CA.

The beneficial reuse of dredged sediment is one strategy in a broader portfolio that is being developed for San Francisco Bay to help marshes adapt to rising sea level. Dredged sediment is currently being used in restoration projects around the Bay, but additional sediment is needed to meet the demand. The guidelines for determining if sediment is appropriate for beneficial reuse were developed twenty years ago. As part of assessing the role of dredged sediment in Bay restoration and adaptation strategies, the Regional Monitoring Program for Water Quality (RMP) and stakeholders recognized the need to revisit the beneficial reuse guidelines for dredged sediment. In September 2019, the RMP convened a workshop that included four technical experts to review the beneficial reuse guidelines. The experts were asked to answer three questions: 1) Are the current screening guidelines appropriate for beneficial reuse? 2) Is the current screening process appropriate and adequate? If not, what are your recommendations for improving it? and 3) How should bioaccumulation potential be addressed for the beneficial reuse of sediment? Based on the discussion of these three questions, six recommendations emerged from the workshop.

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Cohen, A. N. 1999. Extent and impacts of ballast water invasions. SFEI Contribution No. 326. West Coast Ballast Outreach Project: Davis, CA. Vol. 1, pp 2-3.
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Novick, E.; Senn, D. B. 2014. External Nutrient Loads to San Francisco Bay. SFEI Contribution No. 704. San Francisco Estuary Institute: Richmond, CA. p 98.
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Schoellhamer, D. H. 1996. Factors affecting suspended-solids concentrations in South San Francisco Bay, California. Journal of Geophysical Research 101, 12,087-12,095 . SFEI Contribution No. 10.
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Shimabuku, I.; Pearce, S.; Trowbridge, P.; Franz, A.; Yee, D.; Salop, P. 2018. Field Operations Manual for the Regional Monitoring Program. SFEI Contribution No. 902. San Francisco Estuary Institute: Richmond, CA.
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Salop, P.; Bell, D.; Gold, J. 1999. Field Sampling Manual for the RMP for Trace Substances (version 1, January 1999). SFEI Contribution No. 324. San Francisco Estuary Institute: Richmond, CA.
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Collins, J. N. 2001. Final Draft Master List of NIS Plant Species. SFEI Contribution No. 366. San Francisco Estuary Institute.
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Collins, J. N.; Grosso, C. 2004. First Annual Report of the Montezuma Wetlands Restoration Project Technical Review Team. SFEI Contribution No. 102. San Francisco Estuary Institute: Oakland, CA.
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Josh Collins; Lowe, S. 2016. Framework to coordinate water quality improvement and wildlife habitat conservation to protect California streams, wetlands, and riparian areas.

Project funded by an USEPA Wetland Program Development Grant (Region 9) #99T05901: Framework for Coordinated Assessment of CA Wildlife Habitat and Aquatic Resource Areas

. SFEI Contribution No. 776. San Francisco Estuary Institute: Richmond, CA. p 89.

The emergence of comparable landscape approaches to wildlife conservation and water quality improvement through federal and California state regulatory and management programs provides an opportunity for their coordination to better protect California’s aquatic resources, especially streams, wetlands, and riparian areas. Such coordination is patently desirable.  A framework has been developed to help coordinate restoration and compensatory mitigation across policies governing wildlife conservation and water quality in the landscape context. The framework is based on the Wetland and Riparian Area Monitoring Plan (WRAMP) of the California Wetland Monitoring Workgroup (CWMW) of the Water Quality Monitoring Council. The framework presented in this memorandum is a version of the standard WRAMP framework. It only differs from the standard framework to better accommodate wildlife conservation planning, assessment and reporting. To distinguish this version from the standard version, it is termed the 'WRAMP for wildlife'.

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Connor, M. S.; Montagna, P. A.; Alber, M.; Doering, P. 2002. Freshwater inflow: Science, Policy, and Managment. Estuaries 25, 1243-1245 . SFEI Contribution No. 271.
Beller, E. E.; Downs, P. W.; Grossinger, R. M.; Orr, B. K.; Salomon, M. 2016. From past patterns to future potential: using historical ecology to inform river restoration on an intermittent California river. Landscape Ecology 31 (3), 20.

Context  Effective river restoration requires understanding a system’s potential to support desired functions. This can be challenging to discern in the modern landscape, where natural complexity and heterogeneity are often heavily suppressed or modified. Historical analysis is therefore a valuable tool to provide the long-term perspective on riverine patterns, processes, and ecosystem change needed to set appropriate environmental management goals and strategies.

Objective In this study, we reconstructed historical (early 1800s) riparian conditions, river corridor extent, and dry-season flow on the lower Santa Clara River in southern California, with the goal of using this enhanced understanding to inform restoration and management activities.

Method Hundreds of cartographic, textual, and visual accounts were integrated into a GIS database of historical river characteristics.

Results We found that the river was characterized by an extremely broad river corridor and a diverse mosaic of riparian communities that varied by reach, from extensive ([100 ha) willow-cottonwood forests to xeric scrublands. Reach-scale ecological heterogeneity was linked to local variations in dry-season water availability, which was in turn underpinned by regional geophysical controls on groundwater and surface flow.

Conclusions Although human actions have greatly impacted the river’s extent, baseflow hydrology, and riparian habitats, many ecological attributes persist in more limited form, in large part facilitated by these fundamental hydrogeological controls. By drawing on a heretofore untapped dataset of spatially explicit and long-term environmental data, these findings improve our understanding of the river’s historical and current conditions and allow the derivation of reach-differentiated restoration and management opportunities that take advantage of local potential.

Wu, Y.; Tan, H.; Sutton, R.; Chen, D. 2017. From Sediment to Top Predators: Broad Exposure of Polyhalogenated Carbazoles in San Francisco Bay (U.S.A.). Environmental Science and Technology 51, 2038-2046.

The present study provides the first comprehensive investigation of polyhalogenated carbazoles (PHCZ) contamination in an aquatic ecosystem. PHCZs have been found in soil and aquatic sediment from several different regions, but knowledge of their bioaccumulation and trophodynamics is extremely scarce. This work investigated a suite of 11 PHCZ congeners in San Francisco Bay (United States) sediment and organisms, including bivalves (n = 6 composites), sport fish (n = 12 composites), harbor seal blubber (n = 18), and bird eggs (n = 8 composites). The most detectable congeners included 3,6-dichlorocarbazole (36-CCZ), 3,6-dibromocarbazole (36-BCZ), 1,3,6-tribromocarbazole (136-BCZ), 1,3,6,8-tetrabromocarbazole (1368-BCZ), and 1,8-dibromo-3,6-dichlorocarbazole (18-B-36-CCZ). The median concentrations of ΣPHCZs were 9.3 ng/g dry weight in sediment and ranged from 33.7 to 164 ng/g lipid weight in various species. Biomagnification was observed from fish to harbor seal and was mainly driven by chlorinated carbazoles, particularly 36-CCZ. Congener compositions of PHCZs differed among species, suggesting that individual congeners may be subject to different bioaccumulation or metabolism in species occupying various trophic levels in the studied aquatic system. Toxic equivalent (TEQ) values of PHCZs were determined based on their relative effect potencies (REP) compared to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The median TEQ was 1.2 pg TEQ/g dry weight in sediment and 4.8 – 19.5 pg TEQ/g lipid weight in biological tissues. Our study demonstrated the broad exposure of PHCZs in San Francisco Bay and their characteristics of bioaccumulation and biomagnification along with dioxin-like effects. These findings raise the need for additional research to better elucidate their sources, environmental behavior, and fate in global environments.

Yarnell, S. M.; Petts, G. E.; Schmidt, J. C.; Whipple, A. A.; Beller, E. E.; Dahm, C. N.; Goodwin, P.; Viers, J. H. 2015. Functional Flows in Modified Riverscapes: Hydrographs, Habitats and Opportunities. BioScience.

Building on previous environmental flow discussions and a growing recognition that hydrogeomorphic processes are inherent in the ecological functionality and biodiversity of riverscapes, we propose a functional-flows approach to managing heavily modified rivers. The approach focuses on retaining specific process-based components of the hydrograph, or functional flows, rather than attempting to mimic the full natural flow regime. Key functional components include wet-season initiation flows, peak magnitude flows, recession flows, dry-season low flows, and interannual variability. We illustrate the importance of each key functional flow using examples from western US rivers with seasonably predictable flow regimes. To maximize the functionality of these flows, connectivity to morphologically diverse overbank areas must be enhanced in both space and time, and consideration must be given to the sediment-transport regime. Finally, we provide guiding principles for developing functional flows or incorporating functional flows into existing environmental flow frameworks.

Weston, D. P. 1996. Further Development of Chronic Ampelisca Abdita Bioassay as an Indicator of Sediment Toxicity. SFEI Contribution No. 17. San Francisco Estuary Institute: Richmond, CA.
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Cohen, A. N. 1996. Gateway to the Inland Coast: The Story of the Carquinez Strait. California State Lands Commission: Sacramento CA.
Thompson, B.; Chapman, J. 1997. General guidelines for using the sediment quality triad. Mar. Poll. Bull 34, 368-372 . SFEI Contribution No. 198.
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Cohen, A. N.; Weinstein, A.; Carlton, J. T.; Emmett, M. A.; Lau, W. 2005. Global Spread of Marine Organisms in the Baitworm Trade. SFEI Contribution No. 455. San Francisco Estuary Institute: Oakland, CA.
David, N.; McKee, L. J. . 2009. Going Organic Project. SFEI Contribution No. 588. San Francisco Estuary Institute: Oakland, Ca.
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