Kauhanen, P.; Grosso, C.; Salomon, M.; Braud, A. 2023. Delta Aquatic Resources Inventory (DARI): Mapping Methods and Standards for Channels, Wetlands, and Riparian Areas in the Sacramento-San Joaquin River Delta v1.0.

Lowe, J.; Plane, E.; Gonzalez, J.; Salomon, M. 2021. Guidance for Restoration of Natural and Nature-Based Features in the Wetland-Upland Transition Zone. San Francisco Estuary Institute, California State Coastal Conservancy: Richmond, CA.

Baumgarten, S. A.; Hagerty, S.; Vaughn, L. Smith; Spotswood, E.; Grossinger, R. M.; Beller, E. E.; Salomon, M.; Clark, E.; Stoneburner, L. 2021. Peninsula Watershed Historical Ecology Study.  SFEI Contribution No. 1029. San Francisco Estuary Institute: Richmond, Ca.

Lowe, S. 2020. Santa Clara County Five Watersheds Assessment: A Synthesis of Ecological Data Collection and Analysis Conducted by Valley Water.  Pearce, S., Salomon, M., Collins, J., Titus, D., Eds..  SFEI Contribution No. 963. San Francisco Estuary Institute: Richmond. CA. p 71.
This report synthesizes the baseline assessments for Santa Clara County?s five watersheds to present similarities, differences, and compare ecological condition in streams across watersheds and their subregions, San Francisco Bay-Delta ecoregion, and statewide based on CRAM. It also interprets the assessment results and comparisons to identify risks to stream conditions, and opportunities for stream stewardship. Project D5?s baseline assessments establish a monitoring and assessment framework for evaluating the performance of Valley Water?s programs, projects, maintenance activities, and on-the-ground stewardship actions.

Lowe, S. 2019. West Valley Watershed Assessment 2018: Baseline Ecological Condition Assessment of Southwest San Francisco Bay Creeks in Santa Clara County; Calabazas, San Tomas Aquino, Saratoga,  Sunnyvale East and West.  Salomon, M., Pearce, S., Josh Collins, Titus, D., Eds..  SFEI Contribution No. 944. San Francisco Estuary Institute: Richmond.
This report describes baseline information about the amount and distribution of aquatic resources, and evaluates the overall ecological conditions of streams using the California Rapid Assessment Method (CRAM), for the West Valley watershed in Santa Clara County; consisting of Sunnyvale East and West Channels, Calabazas Creek, San Tomas Aquino and Saratoga creeks, and many smaller tributaries.

Beagle, J.; Richey, A.; Hagerty, S.; Salomon, M. 2018. Observational Study of Sycamore Regeneration at two sites in Santa Clara County after the 2016-2017 Water Year.  SFEI Contribution No. 874.

Richey, A.; Dusterhoff, S. D.; McKnight, K.; Salomon, M.; Hagerty, S.; Askevold, R. A.; Grossinger, R. M. 2018. Resilient Landscape Vision for Upper Penitencia Creek.  SFEI Contribution No. 894. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.

Schoellhamer, D.; McKee, L.; Pearce, S.; Kauhanen, P.; Salomon, M.; Dusterhoff, S.; Grenier, L.; Marineau, M.; Trowbridge, P. 2018. Sediment Supply to San Francisco Bay.  SFEI Contribution No. 842. San Francisco Estuary Institute : Richmond, CA.

Lowe, S. 2017. Lower Peninsula Watershed Condition Assessment 2016: Southwest San Francisco Bay, Santa Clara County, San Francisquito to Stevens Creeks. Technical memorandum prepared for the Santa Clara Valley Water District.  Salomon, M., Pearce, S., Josh Collins, Titus, D., Eds..  SFEI Contribution No. 809. San Francisco Estuary Institute: Richmond. p 53.

Beagle, J.; Richey, A.; Hagerty, S.; Salomon, M.; Askevold, R. A.; Grossinger, R. M.; Reynolds, P.; McClain, C.; Spangler, W.; Quinn, M.; et al. 2017. Sycamore Alluvial Woodland: Habitat Mapping and Regeneration Study.  SFEI Contribution No. 816.
This study investigates the relative distribution, health, and regeneration patterns of two major stands of sycamore alluvial woodland (SAW), representing managed and natural settings. Using an array of ecological and geomorphic field analyses, we discuss site characteristics favorable to SAW health and regeneration, make recommendations for restoration and management, and identify next steps. Findings from this study will contribute to the acquisition, restoration, and improved management of SAW as part of the Santa Clara Valley Habitat Plan (VHP).

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.

Doehring, C.; Beagle, J.; Lowe, J.; Grossinger, R. M.; Salomon, M.; Kauhanen, P.; Nakata, S.; Askevold, R. A.; Bezalel, S. N. 2016. San Francisco Bay Shore Inventory: Mapping for Sea Level Rise Planning.  SFEI Contribution No. 779. San Francisco Estuary Institute: Richmond, CA.
With rising sea levels and the increased likelihood of extreme weather events, it is important for regional agencies and local municipalities in the San Francisco Bay Area to have a clear understanding of the status, composition, condition, and elevation of our current Bay shore, including both natural features and built infrastructure.
<br />The purpose of this Bay shore inventory is to create a comprehensive and consistent picture of today?s Bay shore features to inform regional planning. This dataset includes both structures engineered expressly for flood risk management (such as accredited levees) and features that affect flooding at the shore but are not designed or maintained for this purpose (such as berms, road embankments, and marshes). This mapping covers as much of the ?real world? influence on flooding and flood routing as possible, including the large number of non-accredited structures.<br />This information is needed to:
<li>identify areas vulnerable to flooding.</li><li>identify adaptation constraints due to present Bay shore alignments; and</li><li>suggest opportunities where beaches, wetlands, and floodplains can be maintained or restored and integrated into flood risk management strategies.</li>The primary focus of the project is therefore to inform regional planners and managers of Bay shore characteristics and vulnerabilities. The mapping presented here is neither to inform FEMA flood designation nor is it a replacement for site-specific analysis and design.
<br />The mapping consists of two main elements:
<li>Mapping of Bay shore features (levees, berms, roads, railroads, embankments, etc.) which could affect flooding and flood routing.</li><li>Attributing Bay shore features with additional information including elevations, armoring, ownership (when known), among others.</li>SFEI delineated and characterized the Bay shore inland to 3 meters (10ft) above mean higher high water (MHHW) to accommodate observed extreme water levels and the commonly used range of future sea level rise (SLR) scenarios. Elevated Bay shore features were mapped and classified as engineered levees, berms, embankments, transportation structures, wetlands, natural shoreline, channel openings, or water control structures. Mapped features were also attributed with elevation (vertical accuracy of <5cm reported in 30 meter (100ft) segments from LiDAR derived digital elevation models (DEMs), FEMA accreditation status, fortification (e.g., riprap, buttressing), frontage (e.g., whether a feature was fronted by a wetland or beach), ownership, and entity responsible for maintenance. Water control structures, ownership, and maintenance attributes were captured where data was available (not complete for entire dataset). The dataset was extensively reviewed and corrected by city, county, and natural resource agency staff in each county around the Bay. This report provides further description of the Bay shore inventory and methods used for developing the dataset. The result is a publicly accessible GIS spatial database.

Salomon, M.; Dusterhoff, S. D.; Askevold, R. A.; Grossinger, R. M. 2016. San Francisquito Creek Baylands: Landscape Change Metrics Analysis. Flood Control 2.0.  SFEI Contribution No. 784. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA. p 12.
Major Findings<br />Over the past 150 years, lower San Francisquito Creek and the adjacent baylands have been modified for the sake of land reclamation and flood control. This study focused on developing an understanding of the magnitude of habitat change since the mid-19th century through comparisons of key historical and contemporary landscape-scale habitat features, as well as several key landscape metrics that relate to ecological functions and landscape resilience. The major findings from the analyses conducted for this study are as follows:<br />? Historically, the San Francisquito Creek Baylands included a mosaic of habitat types, including an extensive tidal marsh plain with salt pannes and an expansive tidal channel network, a broad bay flat, and a relatively wide contiguous low-gradient tidal-terrestrial transition zone.<br />? Since the late 19th century, a combination of land reclamation and the inland migration of the shoreline has resulted in a 55% decrease in tidal marsh area, a 67% decrease in total tidal channel length, a 40% reduction in channel flat area, a 20% increase in bay flat area, and a 95% decrease in tidal-terrestrial transition zone length.<br />? Land reclamation has also resulted in the creation of new features that did not exist in the area historically including tidal lagoons, non-tidal open water features, and non-tidal wetlands.<br /> 
Recommendations<br />The findings from this study provide insight into the drivers for and magnitude of habitat change within the San Francisquito Creek Baylands, and can therefore help inform climate-resilient approaches for regaining some of the lost landscape features and ecological functions. Specific management recommendations developed from the study findings are as follows:<br />? The dramatic decrease in tidal marsh area and associated tidal channel length since the mid-1800s make tidal marsh restoration a high priority. To make restored areas sustainable over the long-term, restoration should include reestablishing regular tidal inundation as well as reestablishing a connection with San Francisquito Creek and the delivery of freshwater and fine sediment. Restoration efforts should focus on large contiguous areas with minimal infrastructure and should ideally be done sometime over the next decade to ensure the restored areas will have a chance of surviving the sharp increase in the rate of sea level rise that is predicted to occur around 2030 (Goals Update 2015).<br />? Similarly, the dramatic decrease in the tidal-terrestrial transition zone makes it a high priority for any restoration vision for this area. The transition zone provides distinct ecological services and marsh migration space, and is in need of restoration throughout the South Bay. Since most of the upland land along the historical tidal-terrestrial transition zone is currently developed, near-term restoration efforts should focus on creating transition zone habitats on the bayside of flood risk management levees (Goals Update 2015).<br />? The landscape metrics used in this study (tidal habitat area, tidal channel length, and tidal-terrestrial interface length) can be used to help design resilient landscape restoration and adaptation strategies around the mouth of San Francisquito Creek. Specifically, the metrics can be used to assess the long-term ecological benefit associated with various processes-based restoration approaches (i.e., approaches that create habitat features and establish physical processes required for habitat resilience). Additional useful landscape metrics are being developed as part of the Resilient Silicon Valley project (see Robinson et al. 2015).

Jabusch, T.; Bresnahan, P.; Trowbridge, P.; Novick, E.; Wong, A.; Salomon, M.; Senn, D. 2016. Summary and Evaluation of Delta Subregions for Nutrient Monitoring and Assessment.  SFEI Contribution No. 789.

Beagle, J.; Downs, P. W.; Grossinger, R. M.; Orr, B. K.; Salomon, M. 2015. Historical ecology and landscape change in the Sacramento - San Joaquin Delta. HydroLink.

Salomon, M.; Baumgarten, S.; Dusterhoff, S. D.; Beller, E. E.; Askevold, R. A. 2015. Novato Creek Baylands Historical Ecology Study.  SFEI Contribution No. 740. San Francisco Estuary Institute - Aquatic Science Center: Richmond, CA.
Project Background
Over the past century and a half, lower Novato Creek and the surrounding tidal wetlands have been heavily modified for flood control and land reclamation purposes. Levees were built in the tidal portion of the mainstem channel beginning in the late 1800s to convey flood flows out to San Pablo Bay more rapidly and to remove surrounding areas from inundation. Following levee construction, the wetlands surrounding the channel were drained and converted to agricultural, residential, and industrial areas. These changes have resulted in a considerable loss of wetland habitat, reduced sediment transport to marshes and the Bay, and an overall decreased resilience of the system to sea level rise.<br />In addition to tidal wetland modification, land use changes upstream in the Novato Creek watershed have resulted in several challenges for flood control management. Dam construction and increased runoff in the upper watershed have resulted in elevated rates of channel incision, which have increased transport of fine sediment from the upper watershed to lower Novato Creek. Channelization of tributaries and construction of irrigation ditches have likely increased drainage density in the upper watershed, also potentially contributing to increased rates of channel incision and fine sediment production (Collins 1998). Downstream, sediment transport capacity has been reduced by construction of a railroad crossing and loss of tidal prism and channel capacity associated with the diking of the surrounding marsh. As a result of the increased fine sediment supply from the watershed and the loss of sediment transport capacity in lower Novato Creek, sediment aggradation occurs within the channel, which in turn reduces the flood capacity of the channel, necessitating periodic dredging.
Currently, the Marin County Department of Public Works (MCDPW) is coordinating the Novato Watershed Program, which includes Marin County Flood Control and Water Conservation District, Novato Sanitary District, and North Marin Water District. Within lower Novato Creek, the Program is seeking to implement a new approach to flood control that includes redirecting sediment for beneficial use, reducing flood channel maintenance costs, restoring wetland habitat, and enhancing resilience to sea level rise. Included as part of this goal is the re-establishment of historical physical processes that existed before major channel modification, which in turn will re-establish historical ecological functions and help to create a tidal landscape that is resilient to increasing sea level.

Grossinger, R. M.; Dusterhoff, S. D.; Doehring, C.; Salomon, M.; Askevold, R. A. 2015. Novato Creek Baylands Vision: Integrating ecological functions and flood protection within a climate-resilient landscape.  SFEI Contribution No. 764.
This report explores the potential for integrating ecological functions into flood risk management on lower Novato Creek. It presents an initial vision of how ecological elements could contribute to flood protection, based on a broad scale analysis and a one day workshop of local and regional experts. The Vision is not intended to be implemented as is, but rather adapted and applied through future projects and analysis. Other actions (e.g., floodwater detention basins) may also need to be implemented in the interim to meet flood risk objectives.

Lowe, S.; Salomon, M. 2015. Project: Statistical Design, Analysis and Guidance on the Pajaro and Lower Peninsula Watershed Assessments. TASK 2: Basis of Assessment Memorandum ? Review Existing GIS Data & Develop Stream Assessment Study Designs for the Pajaro and Lower Peninsula Wate.  SFEI Contribution No. 762.

Beagle, J.; Salomon, M.; Grossinger, R. M.; Baumgarten, S.; Askevold, R. A. 2015. Shifting Shores: Marsh Expansion and Retreat in San Pablo Bay.  SFEI Contribution No. 751.
EXECUTIVE SUMMARY<br />As sea level rise accelerates, our shores will be increasingly vulnerable to erosion. Particular concern centers around the potential loss of San Francisco Bay?s much-valued tidal marshes, which provide natural flood protection to our shorelines, habitat for native wildlife, and many other ecosystem services. Addressing this concern, this study is the first systematic analysis of the rates of marsh retreat and expansion over time for San Pablo Bay, located in the northern part of San Francisco Bay.
Key findings:<br />? Over the past two decades, more of the marshes in San Pablo Bay have expanded (35% by length) than retreated (6%).<br />? Some areas have been expanding for over 150 years.<br />? Some marsh edges that appear to be retreating are in fact expanding rapidly at rates of up to 8 m/yr.<br />? Marsh edge change may be a useful indicator of resilience, identifying favorable sites for marsh persistence.<br />? These data can provide a foundation for understanding drivers of marsh edge expansion and retreat such as wind direction, wave energy, watershed sediment supply, and mudflat shape.<br />? This understanding of system dynamics will help inform management decisions about marsh restoration and protection.<br />? This study provides a baseline and method for tracking marsh edge response to current and future conditions, particularly anticipated changes in sea level, wave energy, and sediment supply.
<br />Recommended next steps:<br />? This pilot study for San Pablo Bay marshes should be extended to other marshes in San Francisco Bay.<br />? These initial marsh expansion and retreat findings should be further analyzed and interpreted to improve our understanding of system drivers and identify management responses.<br />? A program for repeated assessment should be developed to identify and track changes in shoreline position, a leading indicator of the likelihood marsh survival.

Lowe, S.; Grosso, C.; Pearce, S.; Robinson, A.; Salomon, M.; Kauhanen, P.; Shusterman, G.; Bezalel, S. N.; Collins, J. N.; Titus, D.; et al. 2015. Stream Health of the Coyote Creek and Guadalupe River Watersheds using WRAMP.

Baumgarten, S.; Beller, E. E.; Grossinger, R. M.; Striplen, C. J.; Brown, H.; Dusterhoff, S. D.; Salomon, M.; Askevold, R. A. 2014. Historical Changes in Channel Alignment along Lower Laguna de Santa Rosa and Mark West Creek. SFEI: Richmond, CA.

Stein, E. D.; Cayce, K.; Salomon, M. N.; Bram, D. L.; De Mello, D.; Grossinger, R. M.; Dark, S. 2014. Wetlands of the Southern California Coast: Historical Extent and Change Over Time.  SFEI Contribution No. 720. Southern California Coastal watershed Research Project (SCCWRP), San Francisco Estuary Institute (SFEI), CSU Northridge Center for Geographical Studies: Costa Mesa, Richmond, Northridge.

Stanford, B.; Grossinger, R. M.; Beagle, J.; Askevold, R. A.; Leidy, R. A.; Beller, E. E.; Salomon, M.; Striplen, C. J.; Whipple, A. 2013. Alameda Creek Watershed Historical Ecology Study. San Francisco Estuary Institute: Richmond, CA.

Beller, E. E.; Salomon, M.; Grossinger, R. M. 2013. An Assessment of the South Bay Historical Tidal-Terrestrial Transition Zone.  SFEI Contribution No. 693. San Francisco Estuary Institute: Richmond, CA.

Grossinger, R. M.; Dusterhoff, S. D.; Salomon, M. 2013. Flood Control 2.0 Regional Forum: Novato Creek Flood Control Project.

Whipple, A.; Askevold, R. A.; Rankin, D.; Stanford, B.; Salomon, M. 2012. Delta Historical Ecology GIS Data.

Grossinger, R. M.; Askevold, R. A.; Beagle, J.; Beller, E. E.; Brewster, E.; Gardner, S.; Pearce, S.; Ruygt, J.; Salomon, M.; Striplen, C. J.; et al. 2012. Napa Valley Historical Ecology Atlas: Exploring a Hidden Landscape of Transformation and Resilience. UC Press: Berkeley. p 223.

Beller, E. E.; Grossinger, R. M.; Nicholson, M.; Salomon, M. 2012. Upper Penitencia Creek Historical Ecology Assessment.  SFEI Contribution No. 664. SFEI: Richmond, CA.

Sowers, J. M.; Salomon, M. N.; Ticci, M.; Beller, E. E.; Grossinger, R. M. 2012. Watching Our Watersheds: Santa Clara Valley Past, Google Earth KMZ files: Santa Clara Valley historical points of interest, stream courses and habitats.

Salomon, M.; San Francisco Estuary Institute; Costa, Cof Contra. 2011. Contra Costa County 1939 Aerial Photomosaic, GIS layer containing orthorectified historical aerial imagery of Contra Costa County from 1939.

Stanford, B.; Grossinger, R. M.; Askevold, R. A.; Whipple, A.; Leidy, R. A.; Beller, E. E.; Salomon, M. N.; Striplen, C. J. 2011. East Contra Costa Historical Ecology Study.  SFEI Contribution No. 648. SFEI: Oakland.

Askevold, R. A.; Whipple, A.; Grossinger, R. M.; Stanford, B.; Salomon, M. N. 2011. East Contra Costa Historical Ecology Study GIS data, GIS data produced for the East Contra Costa County Historical Ecology Study.

Beller, E. E.; Grossinger, R. M.; Salomon, M.; Dark, S.; Stein, E.; Orr, B. K.; Downs, P. W.; Longcore, T.; Coffman, G.; Whipple, A.; et al. 2011. Historical Ecology of the lower Santa Clara River, Ventura River, and Oxnard Plain: an analysis of terrestrial, riverine, and coastal habitats.  SFEI Contribution No. 641. SFEI: Oakland.

Salomon, M.; Grossinger, R. M.; Askevold, R. A.; Beller, E. E.; Whipple, A. 2011. Santa Clara Valley Historical Ecology GIS Data.

Grossinger, R. M.; Salomon, M.; Beller, E. E.; Stanford, B.; Whipple, A. 2011. Ventura Historical Ecology Study GIS data.

Beller, E. E.; Salomon, M.; Grossinger, R. M. 2010. Historical Vegetation and Drainage Patterns of Western Santa Clara Valley: A technical memorandum describing landscape ecology in Lower Peninsula, West Valley, and Guadalupe Watershed Management Areas.  SFEI Contribution No. 622. SFEI: Oakland.

Salomon, M.; Collins, J. N.; Striplen, C. J.; Brewster, E.; Grossinger, R. M. 2008. The Historical Ecology of Miller Creek http://www.nbwatershed.org/millercreek/.

Salomon, M.; Grossinger, R. M.; Dawson, A.; Askevold, R. A. 2008. An Introduction to the Historical Ecology of the Sonoma Creek Watershed: a Tool for the Critical Coastal Area Action Plan. San Francisco Estuary Institute.

Grossinger, R. M.; Beller, E. E.; Salomon, M.; Whipple, A.; Askevold, R. A.; Striplen, C. J.; Brewster, E.; Leidy, R. A. 2008. South Santa Clara Valley Historical Ecology Study, including Soap Lake, the Upper Pajaro River, and Llagas, Uvas-Carnadero, and Pacheco Creeks.

Beller, E. E.; Whipple, A.; Askevold, R. A.; Grossinger, R. M.; Fateman, A.; Kopchik, J.; Striplen, C. J.; McRose, D.; Salomon, M. 2007. East Contra Costa County Historical Ecology Study: Introductory Brochure.

Grossinger, R. M.; Salomon, M.; Striplen, C. J.; Beller, E. E.; Askevold, R. A. 2007. Historical Ecology of South Santa Clara County: Preliminary Findings. A Technical Memorandum to the Santa Clara Valley Habitat Conservation Plan/Natural Community Conservation Plan.  SFEI Contribution No. 527.