Dusterhoff, S.; Whipple, A.; Baumgarten, S.; Robinson, A.; Shaw, S.; Stark, K.; Askevold, R. 2023. Restoration Plan for the Laguna de Santa Rosa.  SFEI Contribution No. 1123. San Francisco Estuary Institute: Richmond, CA.
The Laguna de Santa Rosa is an expansive freshwater wetland complex that hosts a rich diversity of plant and wildlife species, and is also home to a thriving agricultural community. Since the mid-19th century, modifications to the Laguna and its surrounding landscape have degraded habitat conditions for both wildlife and people. Together with partners at the Laguna de Santa Rosa Foundation, and funded by Sonoma Water and the California Department of Fish and Wildlife, the goal of the Laguna de Santa Rosa Master Restoration Plan project is to develop a plan that supports ecosystem services in the Laguna?through the restoration and enhancement of landscape processes that form and sustain habitats and improve water quality?while considering flood management issues and the productivity of agricultural lands. 
The first phase of the project was the creation of the Restoration Vision for the Laguna de Santa Rosa. The report details a long-term vision for the landscape which highlights opportunities for multi-benefit habitat restoration and land management within the Laguna?s 100-year floodplain. It presents an understanding of the landscape functioning from past, present, and potential future perspectives. Starting with a picture of the historical ecology of the Laguna that details the magnitude of change in habitat conditions over the past two centuries, the document then presents an understanding of key physical processes that affect today?s Laguna. The restoration concepts described in the Vision represent a potential future Laguna, and were developed and vetted through a series of workshops in which technical advisers, management advisers, tribal representatives, and local landowners and stakeholders shared their expertise and helped shape the concepts. 
The second phase of this project was the development of a Restoration Plan for the Laguna de Santa Rosa that was built from the Vision. The Restoration Plan was developed through a collaborative process that focused on moving forward identified restoration opportunities into conceptual designs that can be used to establish implementable restoration projects. The Restoration Plan includes the following elements:
·	A restoration framework that offers a planning structure for landscape scale restoration that can be further developed and refined over time.
·	Restoration project concepts in the Laguna?s 100-year floodplain developed from selected restoration opportunity areas shown in the Vision.
·	Criteria for prioritizing and sequencing restoration project concepts.utilization of the Restoration Plan and the ultimate success of restoration efforts in the Laguna will require local landowner support and adequate funding to implement the restoration and manage and sustain the benefits through long-term stewardship. It will also require coordination among all the agencies responsible for managing the land and water within the Laguna and its surrounding watershed. With commitment and collaboration the Laguna

Pearce, S.; Whipple, A.; Harris, K.; Lee, V.; Hegstad, R.; McClain, C. 2023. Sycamore Alluvial Woodland Restoration and Enhancement Suitability Study. In collaboration with Alameda County Flood Control and Water Conservation District, Zone 7. Prepared for the US Environmental Protection Agency?s Water Quality Improvement Fund.  SFEI Contribution No. 1128. San Francisco Estuary Institute: Richmond, CA.
The ?Sycamore Alluvial Woodland Restoration and Enhancement Suitability Study? addresses distribution and regeneration patterns and restoration strategies of sycamore alluvial woodland (SAW) habitat, a unique and relatively rare native vegetation community adapted to California?s intermittent rivers and streams. The report was produced by SFEI and H. T. Harvey & Associates, as part of the US EPA Water Quality Improvement Fund Preparing for the Storm grant, led by Zone 7 Water Agency.

Whipple, A.; Robinson, A.; Safran, S. M. 2022. ELEVATION AND OPPORTUNITY IN THE DELTA: Restoring the right thing in the right place.  SFEI Contribution No. 1082. San Francisco Estuary Institute: Richmond, Ca.

A future Sacramento-San Joaquin Delta and Suisun Marsh (?Delta? herein) that supports healthy ecosystems and native species, while also meeting flood risk reduction, water supply, water quality, carbon sequestration, economic, and cultural objectives, requires that appropriate restoration and management actions be taken in the right place at the right time. Geographic setting affects the potential opportunities available?not all actions are suitable everywhere. Physical factors determining what types of activities are appropriate now and in the future include a site?s elevation, degree of tidal and fluvial influence, salinity, soil type, and local effects of climate change, which all vary spatially across the Delta. While there has been considerable progress over the last several decades, continued acceleration of the pace and scale of enhancement actions appropriate to landscape position is needed. Understanding the physical template is necessary for developing strategies that move beyond opportunistic restoration, support resilience over time, and have the potential to connect and magnify benefits across the larger landscape.

Whipple, A.; Grenier, L.; Safran, S. M.; Zeleke, D.; Wells, E.; Deverel, S.; Olds, M.; Cole, S.; Rodríguez-Flores, J.; Guzman, A.; et al. 2022. RESILIENT STATEN ISLAND: Landscape Scenario Analysis Pilot Application.  SFEI Contribution No. 1083. San Francisco Estuary Institute: Richmond, Ca.
A central motivating question for the Sacramento-San Joaquin Delta science and management community is what should be done, where and when, to support future Delta landscapes that are ecologically and economically viable and resilient to change. Actions must be taken that have the greatest potential for achieving multiple benefits. This is especially important given the urgency to rapidly transition Delta landscapes to address biodiversity loss, erosion of ecosystem resilience, flood risk, water supply reliability, and cultural and economic sustainability. Landscape-scale planning is needed to examine how individual actions add up to meaningful change. Such planning involves figuring out how different areas can provide different functions at different times and helps show how choices made now can help shift trajectories toward desired outcomes. Too often, land use and management decisions are made based on a limited set of objectives or at the site scale, resulting in missed opportunities. Actions (or inaction) should not foreclose on critical opportunities. Moving forward, there is great need to more effectively compare possible future scenarios across a range of ecological and economic factors. This scenario analysis for Staten Island ? a large Delta island managed for multiple uses and facing challenges similar to elsewhere in the Delta ? provides an approach to help address this need.

Zi, T.; Kauhanen, P.; Whipple, A.; Mckee, L. 2021. Green Stormwater Infrastructure Planning-level Analysis for Livermore-Amador Valley.  SFEI Contribution No. 1063. San Francisco Estuary Institute: Richmond, Calif.
This effort is intended to provide planning-level regional guidance for placement of green stormwater infrastructure (GSI) in Livermore-Amador Valley. This work identifies potential GSI locations and quantifies contaminant load and stormwater runoff volume reduction benefits through the application of GreenPlan-IT, a planning tool developed by the San Francisco Estuary Institute and regional partners. Ultimately, the urban greening analysis presented in this report is intended to help enhance stream and watershed resilience, reduce peak flows, and improve water quality.

Cloern, J. E.; Safran, S. M.; Vaughn, L. Smith; Robinson, A.; Whipple, A.; Boyer, K. E.; Drexler, J. Z.; Naiman, R. J.; Pinckney, J. L.; Howe, E. R.; et al. 2021. On the human appropriation of wetland primary production. Science of the Total Environment 785.
Humans are changing the Earth's surface at an accelerating pace, with significant consequences for ecosystems and their biodiversity. Landscape transformation has far-reaching implications including reduced net primary production (NPP) available to support ecosystems, reduced energy supplies to consumers, and disruption of ecosystem services such as carbon storage. Anthropogenic activities have reduced global NPP available to terrestrial ecosystems by nearly 25%, but the loss of NPP from wetland ecosystems is unknown. We used a simple approach to estimate aquatic NPP from measured habitat areas and habitat-specific areal productivity in the largest wetland complex on the USA west coast, comparing historical and modern landscapes and a scenario of wetland restoration. Results show that a 77% loss of wetland habitats (primarily marshes) has reduced ecosystem NPP by 94%, C (energy) flow to herbivores by 89%, and detritus production by 94%. Our results also show that attainment of habitat restoration goals could recover 12% of lost NPP and measurably increase carbon flow to consumers, including at-risk species and their food resources. This case study illustrates how a simple approach for quantifying the loss of NPP from measured habitat losses can guide wetland conservation plans by establishing historical baselines, projecting functional outcomes of different restoration scenarios, and establishing performance metrics to gauge success.

Pearce, S.; Mckee, L.; Whipple, A.; Church, T. 2021. Towards a Coarse Sediment Strategy for the Bay Area.  SFEI Contribution No. 1032. San Francisco Estuary Institute: Richmond, CA.
Historic and current regional management of watersheds and channels for water supply and flood control across the San Francisco Bay Area has cut off much of the coarse sediment that was historically delivered to the Bay. Here we define coarse sediment as having grain sizes larger than 0.0625 mm, which includes sand, gravel and even cobble, as opposed to fine sediment that includes clay, mud and silt. Future projections indicate that sediment supply will not meet the demand from extant and restored tidal marshes to keep up with sea level rise.
<br />The US EPA Water Quality Improvement Fund Preparing for the Storm grant has funded the Zone 7 Water Agency, the San Francisco Estuary Institute and the San Francisco Bay Joint Venture to support the future development of a successful regional coarse sediment reuse strategy. Development of such a strategy requires an understanding of logistical and regulatory hurdles and identification of key strategies for breaking down barriers. One potential solution for meeting the sediment demand along the Bay margin is to utilize coarse sediment that is removed from flood control channels by public agencies. To-date, very little of this sediment that is removed is beneficially reused for restoration along the Bay shoreline. The current economic and regulatory framework around sediment removal presents many challenges, barriers and lack of incentives for agencies to reuse their sediment.
This document represents a step forward towards beneficially reusing coarse flood control channel sediment by outlining reuse challenges, and identifying incentives for participation and potential solutions.

Zi, T.; Whipple, A.; Kauhanen, P.; Spotswood, E.; Grenier, L.; Grossinger, R.; Askevold, R. 2021. Trees and Hydrology in Urban Landscapes.  SFEI Contribution No. 1034. San Francisco Estuary Institute: Richmond, CA.
Effective implementation of urban greening strategies is needed to address legacies of landscape change and environmental degradation, ongoing development pressures, and the urgency of the climate crisis. With limited space and resources, these challenges will not be met through single-issue or individual-sector management and planning. Increasingly, local governments, regulatory agencies, and other urban planning organizations in the San Francisco Bay Area are expanding upon the holistic, portfolio-based, and multi-benefit approaches.
This effort, presented in the Trees and Hydrology in Urban Landscapes report, seeks to build links between stormwater management and urban ecological improvements by evaluating how complementary urban greening activities, including green stormwater infrastructure (GSI) and urban tree canopy, can be integrated and improved to reduce runoff and contaminant loads in stormwater systems. This work expands the capacity for evaluating engineered GSI and non-engineered urban greening within a modeling and analysis framework, with a primary focus on evaluating the hydrologic benefit of urban trees. Insights can inform stormwater management policy and planning. 

Vaughn, L. Smith; Safran, S.; Robinson, A.; Whipple, A.; Richey, A.; Grenier, L.; Cloern, J.; Andrews, S.; Boyer, K.; Drexler, J.; et al. 2020. Delta Landscapes Primary Production: Past, Present, Future.  SFEI Contribution No. 988. San Francisco Estuary Institute: Richmond, CA.
This report describes the Delta Landscapes Primary Production project, which quantifies how landscape change in the Delta has altered the quantity and character of primary production. Combining historical and modern maps with simple models of production for five dominant plant and algae groups, we estimate primary production across the hydrologically connected Delta. We evaluate changes in primary production over time (between the early 1800s and early 2000s), between wet and dry years, and with future targets for landscape-scale restoration. For managers in the Delta, restoring historical patterns of primary productivity is a means to better support native fish and other wildlife. To better equip decision makers in managing for improved primary production, this study offers historical context and the best available science on the relative production value of habitat types and their configurations. 

Panlasigui, S.; Pearce, S.; Hegstad, R.; Quinn, M.; Whipple, A. 2020. Wildlife Habitat and Water Quality Enhancement Opportunities at Castlewood Country Club.  SFEI Contribution No. 1003. San Francisco Estuary Institute: Richmond, CA.
Meeting human and ecological needs within San Francisco Bay?s watersheds is increasingly challenged by flooding, water quality degradation, and habitat loss, exacerbated by intensified urbanization and climate change. Addressing these challenges requires implementing multi-benefit strategies through new partnerships and increased coordination across the region?s diverse landscapes. Actions to improve water quality and enhance habitat for biodiversity in our highly developed and managed landscapes can help the region as a whole to build resilience to withstand current pressures and future change. The EPA-funded project, ?Preparing for the Storm,? aims to address these challenges at the site- and landscape-scale through studies and implementation projects in the Livermore-Amador Valley. As part of this larger project, this technical report presents a synthesis of water quality and habitat improvement opportunities for a golf course of Castlewood Country Club.

Whipple, A.; Grantham, T.; Desanker, G.; Hunt, L.; Merrill, A.; Hackenjos, B.; Askevold, R. A. 2019. Chinook Salmon Habitat Quantification Tool: User Guide (Version 1.0). Prepared for American Rivers. Funded by the Natural Resources Conservation Service Conservation Innovation Grant (#69-3A75-17-40), Water Foundation and Environmental Defense Fund. A report of SFEI-ASC?s Resilient Landscapes Program.  SFEI Contribution No. 953. San Francisco Estuary Institute: Richmond, CA.
The Salmon Habitat Quantification Tool provides systematic, transparent, and consistent accounting of the spatial extent, temporal variability, and quality of salmon habitat on the landscape. It is part of the multi-species assessment of the Central Valley Habitat Exchange (CVHE, www.cvhe.org). The suitability criteria applied in the tool were established by Stillwater Sciences and the Technical Advisory Committee (TAC), and the Chinook salmon HQT habitat evaluation and User Guide development was led by American Rivers and the San Francisco Estuary Institute. The approach uses commonly-applied concepts for evaluating suitable habitat based on modeling, with methods adapted from the hydrospatial analysis approach developed by Alison Whipple (2018).

Church, T.; Beagle, J.; Whipple, A.; Desanker, G.; Richey, A.; Quinn, M.; Hegstad, R. 2019. Sycamore Alluvial Woodland Presence and Distribution.

Cloern, J. E.; Barnard, P. L.; Beller, E. E.; Callaway, J.; Grenier, J. Letitia; Grossinger, R. M.; Whipple, A.; Mooney, H.; Zavaleta, E. 2016. Estuaries: Life on the edge. In Ecosystems of California. Ecosystems of California. University of California Press: Berkeley, CA. pp 359-388.

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.

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.

Beagle, J.; Whipple, A.; Grossinger, R. M. 2013. Landscape Patterns and Processes of the McCormack-Williamson Tract and Surrounding Area: A framework for restoring a resilient and functional landscape.  SFEI Contribution No. 674. SFEI-ASC: Richmond, CA.

Whipple, A.; Grossinger, R. M.; Rankin, D. 2012. Building a Landscape Perspective for the Delta: Lessons from Historical Ecology.

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

Beller, E. E.; Safran, S. M.; Grossinger, R.; Grenier, J. Letitia; Whipple, A.; Beagle, J.; Robinson, A.; Askevold, R. A. 2012. Developing Tools for Landscape-Scale Restoration in the Delta.

Beagle, J.; Whipple, A.; Grossinger, R. M. 2012. Historical Ecology and Landscape-Scale Restoration. Application to the McCormack-Williamson Tract.

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.

Whipple, A.; Grossinger, R. M.; Rankin, D.; Stanford, B.; Askevold, R. A. 2012. Sacramento-San Joaquin Delta Historical Ecology Investigation: Exploring Pattern and Process.  SFEI Contribution No. 672. SFEI: Richmond.
The Sacramento-San Joaquin Delta has been transformed from the largest wetland system on the Pacific Coast of the United States to highly productive farmland and other uses embodying California?s water struggles. The Delta comprises the upper extent of the San Francisco Estuary and connects two-thirds of California via the watersheds that feed into it. It is central to the larger California landscape and associated ecosystems, which will continue to experience substantial modification in the future due to climate change and continued land and water use changes. Yet this vital ecological and economic link for California and the world has<br />been altered to the extent that it is no longer able to support needed ecological functions. Approximately 3% of the Delta?s historical tidal wetland extent remains wetland today; the Delta is now crisscrossed with agricultural ditches replacing the over 1,000 miles of branching tidal channels.
Imagining a healthy Delta ecosystem in the future and taking bold, concrete steps toward that future requires an understanding and vision of what a healthy ecosystem looks like. For a place as extensive, unique, and modified as the Delta, valuable knowledge can be acquired through the study of the past, investigating the Delta as it existed just prior to the substantial human modifications of the last 160 years. Though the Delta is irrevocably altered, this does not mean that the past is irrelevant. Underlying geologic and hydrologic processes still influence the landscape, and native species still ply the waters, soar through the air, and move across the land. Significant opportunities are available to strategically reconnect landscape components in ways that support ecosystem resilience to both present and future stressors.

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.

Whipple, A.; Grossinger, R. M. 2011. Habitat Characteristics of Past Delta Landscapes: Knowledge for Improving Future Ecosystem Resilience.

Grossinger, R. M.; Whipple, A. 2011. Habitat Characteristics that Made Delta Landscapes Unique: Perspectives for Ecosystem Restoration.

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.

Grossinger, R. M.; Stein, E. D.; Cayce, K.; Dark, S.; Askevold, R. A.; Whipple, A. 2011. Historical Wetlands of the Southern California Coast: An Atlas of US Coast Survey T-sheets, 1851-1889.  SFEI Contribution No. 586. 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.

Grossinger, R. M.; Whipple, A.; Rankin, D.; Collins, J. N. 2010. Historical Delta Landscapes: Conceptual models for building a diverse and resilient future.

Whipple, A. 2010. Historical Ecology of the Delta: Habitat characteristics of a fluvial-tidal landscape.

Whipple, A.; Grossinger, R. M.; Rankin, D.; Collins, J. N. 2010. The Historical Yolo Basin Landscape: What parts make the whole?.

Whipple, A.; Grossinger, R. M.; Davis, F. W. 2010. Shifting Baselines in a California Oak Savanna: Nineteenth Century Data to Inform Restoration Scenarios. Restoration Ecology 19 (101), 88-101 . SFEI Contribution No. 593.
For centuries humans have reduced and transformed Mediterranean-climate oak woodland and savanna ecosystems, making it difficult to establish credible baselines for ecosystem structure and composition that can guide ecological restoration efforts. We combined historical data sources, with particular attention to mid-1800s General Land Office witness tree records and maps and twentieth century air photos, to reconstruct 150 years of decline in extent and stand density of Valley oak (Quercus lobata Neé) woodlands and savannas in the Santa Clara Valley of central coastal California. Nineteenth century Valley oak woodlands here were far more extensive and densely stocked than early twentieth century air photos would suggest, although reconstructed basal areas (7.5 m2/ha) and densities (48.9 trees/ha) were not outside the modern range reported for this ecosystem type. Tree densities and size distribution varied across the landscape in relation to soil and topography, and trees in open savannas were systematically larger than those in denser woodlands. For the largest woodland stand, we estimated a 99% decline in population from the mid-1800s to the 1930s. Although most of the study area is now intensely developed, Valley oaks could be reintroduced in urban and residential areas as well as in surrounding rangelands at densities comparable to the native oak woodlands and savannas, thereby restoring aspects of ecologically and culturally significant ecosystems, including wildlife habitat and genetic connectivity within the landscape.

Askevold, R. A.; Fateman, A.; Whipple, A.; Stanford, B.; Grossinger, R. M.; Kopchik, J. 2009. Historical Ecology Informing Restoration in East Contra Costa County: Wetland Restoration Opportunities on a Tributary to Brushy Creek (Souza II Property).

Grossinger, R. M.; Whipple, A. 2009. Historical Ecology of the California Delta: Emerging Concepts of a Complex and Dynamic System.

Beller, E. E.; Grossinger, R. M.; Whipple, A. 2009. Historical Ecology Reconnaissance for the Lower Salinas River.  SFEI Contribution No. 581. San Francisco Estuary Institute: Richmond. p 32.

Grossinger, R. M.; Whipple, A. 2009. Re-Oaking the Valleys: Bringing Native Trees Back into California?s Suburban Landscapes.

Whipple, A.; Grossinger, R. M.; Askevold, R. A. 2008. An Introduction to the Historical Ecology of the Fitzgerald Marine Reserve: a Tool for the Critical Coastal Area Action Plan.

Whipple, A.; Grossinger, R. M.; Askevold, R. A. 2008. An Introduction to the Historical Ecology of the Watsonville Sloughs: a Tool for the Critical Coastal Area Action Plan. San Francisco Estuary Institute.

Whipple, A.; Grossinger, R. M.; Wilcox, C. 2008. Pre-Modification Habitat Mosaics of the Delta: Looking to the Past to Envision the Future.

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.

Beller, E. E.; Whipple, A.; Askevold, R. A.; Grossinger, R. M. 2007. The Historical Ecology of Contra Costa County: An Illustrated Preview and Guide.