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2021
Moore, S.; Hale, T.; Weisberg, S. B.; Flores, L.; Kauhanen, P. 2021. Field Testing Report: California Trash Monitoring Methods. SFEI Contribution No. 1026. San Francisco Estuary Institute: Richmond, Calif.

Trash has received renewed focus in recent years as policy makers, public agencies, environmental organizations, and community groups have taken many steps towards trash quantification and management across California. The range of management actions is matched by the diversity of monitoring approaches, designed to determine key attributes associated with trash pollution on California’s lands and in its waterways.

This report describes the field testing associated with a project designed to validate the accuracy, precision, and practicality of several trash monitoring methods, practiced across the state. Additionally, the project measured the efficacy of a novel monitoring method designed to detect trash via remote sensing and machine learning. Readers will find details about each respective method -- the specific approach to
landscape characterization, the qualitative or quantitative measures undertaken, the team-based quality assurance for data collection -- as well as the approach that the testing team adopted to ensure efficient, accurate, and useful validation of the methods.

Because the validation efforts integrated multiple methods, using multiple teams at a selection of common sites, the field testing report yields useful statistical information not only about each method individually, but about the comparability of the results. The report illustrates the
correlation factor associated with different forms of trash metrics, associated with different methods practiced on the same assessment sites. The results illustrated a generally high degree of correlation among different methods, which promises opportunities to compare results meaningfully across methods.

Furthermore, this field testing report provides quantitative measures to illustrate the repeatability of each method, the differences and insights yielded by assessment site sizing criteria varying among methods, the transferability / teach-ability of each method among trash monitoring practitioners, and how the degrees of accuracy might aid programs in performing mass balance analysis of known sources
to trash detected in a given site.

Regarding innovation, the project team leveraged multiple on-the-ground methods and special testing scenarios to compare conventional and novel (aerial) assessments to measure the relative accuracy and precision of this emergent technology that might address some of the resource constraints that currently limit the broader or more frequent deployment of conventional trash assessment methods. The analyses captured in this field testing report offer specific quantitative measures of the accuracy (bias), precision (repeatability), practicality and cost associated with each method. This information is subsequently used to inform a companion summary analysis found in the Trash Monitoring Playbook, which is designed to evaluate the applicability of the monitoring methods to address classes of
monitoring questions.

 (14.46 MB)
Dusterhoff, S.; Shaw, S.; McKnight, K. 2021. Flood Control Channel Classification Scheme for the San Francisco Bay Region. Josh Collins, Ed.. San Francisco Bay Region Flood Control Channel Classification . SFEI Contribution No. 1046. San Francisco Estuary Institute: Richmond, CA.
 (11.94 MB)
Chang, D.; Richardot, W.; Miller, E.; Dodder, N.; Sedlak, M.; Hoh, E.; Sutton, R. 2021. Framework for nontargeted investigation of contaminants released by wildfires into stormwater runoff: Case study in the northern San Francisco Bay area. Integrated Environmental Assessment and Management . SFEI Contribution No. 1044.

Wildfires can be extremely destructive to communities and ecosystems. However, the full scope of the ecological damage is often hard to assess, in part due to limited information on the types of chemicals introduced to affected landscapes and waterways. The objective of this study was to establish a sampling, analytical, and interpretive framework to effectively identify and monitor contaminants of emerging concern in environmental water samples impacted by wildfire runoff. A nontargeted analysis consisting of comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC × GC/TOF-MS) was conducted on stormwater samples from watersheds in the City of Santa Rosa and Sonoma and Napa Counties, USA, after the three most destructive fires during the October 2017 Northern California firestorm. Chemicals potentially related to wildfires were selected from the thousands of chromatographic features detected through a screening method that compared samples from fire-impacted sites versus unburned reference sites. This screening led to high confidence identifications of 76 potentially fire-related compounds. Authentic standards were available for 48 of these analytes, and 46 were confirmed by matching mass spectra and GC × GC retention times. Of these 46 compounds, 37 had known commercial and industrial uses as intermediates or ingredients in plastics, personal care products, pesticides, and as food additives. Nine compounds had no known uses or sources and may be oxidation products resulting from burning of natural or anthropogenic materials. Preliminary examination of potential toxicity associated with the 46 compounds, conducted via online databases and literature review, indicated limited data availability. Regional comparison suggested that more structural damage may yield a greater number of unique, potentially wildfire-related compounds. We recommend further study of post-wildfire runoff using the framework described here, which includes hypothesis-driven site selection and nontargeted analysis, to uncover potentially significant stormwater contaminants not routinely monitored after wildfires and inform risk assessment. 

2020
 (17.47 MB) (10.87 MB)
2018
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.
 (1.43 MB)
2017
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.

2016
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'.

 (6.62 MB)
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.

2015
 (3.62 MB)
 (31.54 MB) (4.68 MB) (62.4 KB)
Yarnell, S. M.; Petts, G. E.; Schmidt, J. C.; Whipple, 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.

2011
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2001
 (2.3 MB)
Collins, J. N. 2001. Final Draft Master List of NIS Plant Species. SFEI Contribution No. 366. San Francisco Estuary Institute.
 (22.38 KB)
1999
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.
 (412.09 KB)
1996
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.
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.
 (241.1 KB)