Primary Production in the Sacramento-San Joaquin Delta: A Science Strategy to Quantify Change and Identify Future Potential

San Francisco Estuary Institute (SFEI) | May 20th, 2019

Today’s Sacramento-San Joaquin Delta is an unusually low-productivity estuary. The constraints on primary production and the relative importance of different production

Today’s Sacramento-San Joaquin Delta is an unusually low-productivity estuary. The constraints on primary production and the relative importance of different production sources to the food web are major ecological uncertainties in the Delta system. Understanding how the extensive historical changes in the Delta landscape have altered primary production has the potential to inform restoration planning and management across the region.  The Delta Landscapes Project (SFEI-ASC 2014) has recently produced information that allows us, for the first time, to answer questions about historical primary production and carrying capacity from quantified changes in the areal extent and spatial configuration of habitat types in the Delta since the mid-19th century. Our focus is on estimating primary production because the potential capacity of ecosystems to support fish, bird and other wildlife populations is set by primary production – the supply of food required to produce animal biomass. 

Prospect Island Tidal Habitat Restoration Project: Admin Final Restoration Plan

California Department of Water Resources (DWR) | June 12th, 2014

This Prospect Island Tidal Habitat Restoration Project (Project) Draft Restoration Plan (Plan) describes the proposed actions needed to restore up to 1,600 acre (ac) of

This Prospect Island Tidal Habitat Restoration Project (Project) Draft Restoration Plan (Plan) describes the proposed actions needed to restore up to 1,600 acre (ac) of diked lands to tidal wetlands. The Project site is located in Solano County, in the northern Sacramento-San Joaquin River Delta (Delta) (Figure 1-1). Prospect Island falls under two ownerships: the approximately 1,300-ac northern property is owned by the California Department of Water Resources (DWR), and the southern, approximately 300-ac portion is owned by the Port of West Sacramento (Port). There are three privately owned properties contiguous to the site: the Stringer property, a small peninsula connected to the southeast margin of the DWR property; the Hall property, a small peninsula connected to the southeast margin of the Port property; and the Fahn property, actively farmed land north of the Project boundary. A privately operated marina, Arrowhead Harbor, is located at the northeastern corner of the site. With the exception of discussion of site topography (Section 4.3.3), three areal extents are used for the purposes of this Restoration Plan and interrelated environmental analyses of the Project. The Tidal Restoration Footprint is the area internal to the levees that would be subject to tidal action following restoration. The Diked Lands Project Area represents all diked lands that would be restored and potentially used to construct the Project, and extends outward to the high tide line on the exterior side of the levees. The Construction Project Area represents the Diked Lands Project Area plus all potential exterior in-water work areas.

Puzzling Over the Shallows

CALFED | December 1st, 2001

Re-Oaking North Bay: A strategy for restoring native oak ecosystems, focusing on Napa and Sonoma valleys

San Francisco Estuary Institute (SFEI) | July 7th, 2020

Oaks are iconic trees in California, the defining feature of savannas and woodlands in many parts of the state. For millennia, these majestic trees have provided the e

Oaks are iconic trees in California, the defining feature of savannas and woodlands in many parts of the state. For millennia, these majestic trees have provided the ecological foundation upon which thousands of other organisms depend. Their cultural significance is equally profound: they are of central importance to diverse indigenous groups, and are prized for the many benefits they provide California residents. Vast expanses of oak savanna historically occupied the rich alluvial soils of Napa and Sonoma valleys. The immense and long-lived valley oak (Quercus lobata) dominated these savannas, accounting for more than 65% of trees (Dawson 2008, Grossinger et al. 2012). Early observers described the valleys as “studded with groups of oaks” (Marryat 1850), and extolled the “magnificent oaks” that were “the glory of the landscape scenery” (Smith and Elliott 1878). Black oak (Q. kelloggii), coast live oak (Q. agrifolia), and other oak species were present in smaller numbers on the valley floors and were more abundant in the hillsides (Dawson 2008, Grossinger et al. 2012). Over the past two centuries, however, much of this oak savanna has been cleared to make way for orchards, vineyards, and towns. In Napa Valley, the number of mature trees has declined from an estimated 45,000 in the early 1800s to less than 1,000 today (Grossinger et al. 2012). Valley oak habitat has been particularly affected by clearing and fragmentation: in many areas of the state, loss of valley oak woodland exceeds 90% (Kelly et al. 2005, Whipple et al. 2011). Documentation of this loss, and recognition of the value of oaks for both people and nature, has led to a growing desire to restore this unique ecosystem and bring back many of the benefits that oaks provide. Despite the significant changes the North Bay landscape has experienced since European settlement, there are opportunities to restore oaks in settings as diverse as backyards, parks, streets, farms, vineyards, and creeksides.

Re-Oaking Silicon Valley: Building Vibrant Cities with Nature

San Francisco Estuary Institute (SFEI) | August 1st, 2017

In this report, we investigate how integrating components of oak woodlands into developed landscapes — “re-oaking” — can provide an array of valuable functions fo

In this report, we investigate how integrating components of oak woodlands into developed landscapes — “re-oaking” — can provide an array of valuable functions for both wildlife and people. Re-oaking can increase the biodiversity and ecological resilience of urban ecosystems, improve critical urban forest functions such as shade and carbon storage, and enhance the capacity of cities to adapt to a changing climate. We focus on Silicon Valley, where oak woodland replacement by agriculture and urbanization tells a story that has occurred in many other cities in California. We highlight how the history and ecology of the Silicon Valley landscape can be used as a guide to plan more ecologically resilient cities in the Bay Area, within the region and elsewhere in California. We see re-oaking as part of, and not a substitute for, the important and broader oak woodland conservation efforts taking place throughout the state.  

Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California

U.S. Fish and Wildlife Service (FWS) | September 23rd, 2013

The Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California features five endangered species: two endangered animals, California clapper rail (Rallus

The Recovery Plan for Tidal Marsh Ecosystems of Northern and Central California features five endangered species: two endangered animals, California clapper rail (Rallus longirostris obsoletus) and salt marsh harvest mouse (Reithrodontomys raviventris) and three endangered plants, Cirsium hydrophilum var. hydrophilum (Suisun thistle), Chloropyron molle ssp. molle (soft bird’s-beak), and Suaeda californica (California sea-blite). The biology of these species is at the core of the recovery plan, but the goal of this effort is the comprehensive restoration and management of tidal marsh1 ecosystems. This recovery plan is an expansion and revision of The California Clapper Rail and Salt Marsh Harvest Mouse Recovery Plan (U.S. Fish and Wildlife Service 1984). The historic distribution of the California clapper rail encompasses major tidal marshes between Humboldt Bay and Morro Bay, defining the approximate geographic scope of this recovery plan. In addition to the California clapper rail and the salt marsh harvest mouse, the plan also covers three focal listed plant species that were listed as federally endangered in the 1990s and the northernmost population of an additional plant species. Two of the species, Cirsium hydrophilum var. hydrophilum and Chloropyron molle ssp. molle (this species’ former name is Cordylanthus mollis ssp. mollis which is how it appears on the List of Threatened and Endangered Species, but we use the currently accepted name here), are restricted to the northern reaches of the San Francisco Bay Estuary. The other endangered tidal marsh plant, Suaeda californica, historically occurred in both San Francisco Bay and Morro Bay but, except for three reintroductions to San Francisco Bay, is now restricted to Morro Bay. Another federally listed plant, Chloropyron maritimum ssp. maritimum (salt marsh bird’s-beak; formerly Cordylanthus maritimus ssp. maritimus), has its northern range limit in Morro Bay. Morro Bay was omitted from the Salt Marsh Bird’s-beak Recovery Plan (U.S. Fish and Wildlife Service 1985a) because the taxonomic interpretation at the time classified this population in another subspecies that is not federally listed. Current taxonomic interpretation considers the Morro Bay population as Chloropyron maritimum ssp. maritimum. It is included in this recovery plan due to its co-location with Suaeda californica in Morro Bay. Though recovery strategies and actions are provided for the Morro Bay population of C. maritimum ssp. maritimum, recovery criteria are not, therefore, the species should not be considered covered by the recovery portion of the document. In addition, this recovery plan addresses 11 species or subspecies of concern. These include the salt marsh wandering shrew (Sorex vagrans halicoetes), Suisun shrew (Sorex ornatus sinuosus), San Pablo vole (Microtus californicus sanpabloensis), California black rail (Laterallus jamaicensis coturniculus), three song sparrow subspecies of the San Francisco Bay Estuary (Alameda song sparrow [Melospiza melodia ssp. pusillula], Suisun song sparrow [M.m. maxillaris] and San Pablo song sparrow [M.m. samuelis]), saltmarsh common yellowthroat (Geothlypis trichas sinuosa), old man tiger beetle (Cicindela senilis senilis), Lathryrus jepsonii ssp. jepsonii (delta tule pea), and Spartina foliosa (Pacific cordgrass). These species occur in a variety of tidal marsh habitats where they are limited by the requirements of moisture, salinity, topography, soil types, and climatic conditions. Adjacent uplands and ecotone areas are also crucial habitats for many of these species. Primary threats to all the listed species include historical and current habitat loss and fragmentation due to urban development, agriculture, and diking related to duck hunting; altered hydrology and salinity; non-native invasive species; inadequate regulatory mechanisms; disturbance; contamination; risk of extinction due to small population size; and the most central threat, sea level rise due to climate change.

Reducing Methylmercury Accumulation in the Food Webs of San Francisco Bay and Its Local Watersheds

San Francisco Estuary Institute (SFEI) | April 8th, 2014

San Francisco Bay (California, USA) and its local watersheds present an interesting case study in estuarine mercury (Hg) contamination. This review focuses on the most pr

San Francisco Bay (California, USA) and its local watersheds present an interesting case study in estuarine mercury (Hg) contamination. This review focuses on the most promising avenues for attempting to reduce methylmercury (MeHg) contamination in Bay Area aquatic food webs and identifying the scientific information that is most urgently needed to support these efforts.

Reference Guide to On-Farm Groundwater Recharge on Annual Cropland | Recommendations for Creating Waterbird Habitat Benefits

Nature Conservancy | May 1st, 2019

With the Sustainable Groundwater Management Act (SGMA) requiring basins to balance water budgets and manage groundwater sustainably, there is an opportunity to demonstr

With the Sustainable Groundwater Management Act (SGMA) requiring basins to balance water budgets and manage groundwater sustainably, there is an opportunity to demonstrate groundwater recharge with benefits to birds and people. A multiple-benefit approach brings together water managers, farmers, agencies and conservation groups to stabilize groundwater in a manner that provides greater water reliability for farms and communities while protecting ecosystems, including migratory bird habitat.

Reforming Watershed Restoration: Science in Need of Application and Applications in Need of Science (The H.T. Odum Synthesis Essay)

Estuaries and Coasts (Springer) | December 23rd, 2008

Coastal and inland waters are continuing to decline in many parts of the world despite major efforts made to restore them. This is due in part to the inadequate role that

Coastal and inland waters are continuing to decline in many parts of the world despite major efforts made to restore them. This is due in part to the inadequate role that ecological science has played in shaping restoration efforts. A significant amount of fundamental ecological knowledge dealing with issues such as system dynamics, state changes, context-dependency of ecological response, and diversity is both under-used by managers and practitioners and under-developed by ecologists for use in real-world applications. Some of the science that is being ‘used’ has not been adequately tested. Thus, restoration ecology as a science and ecological restoration as a practice are in need of reform. I identify five ways in which our ecological knowledge should be influencing restoration to a far greater extent than at present including a need to: shift the focus to restoration of process and identification of the limiting factors instead of structures and single species, add ecological insurance to all projects, identify a probabilistic range of possible outcomes instead of a reference condition, expand the spatial scale of efforts, and apply hierarchical approaches to prioritization. Prominent examples of restoration methods or approaches that are commonly used despite little evidence to support their efficacy are highlighted such as the use of only structural enhancements to restore biodiversity. There are also major gaps in scientific knowledge that are of immediate need to policy makers, managers, and restoration practitioners including: predictive frameworks to guide the restoration of ecological processes, identification of social-ecological feedbacks that constrain ecosystem recovery and data to support decisions of where and how to implement restoration projects to achieve the largest gains. I encourage ecologists to respond to the demand for their scientific input so that restoration can shift from an engineering-driven process to a more sustainable enterprise that fully integrates ecological processes and social science methods.

Resilient landscape vision for Lower Walnut Creek

San Francisco Estuary Institute (SFEI) | November 30th, 2016

Lower Walnut Creek (Contra Costa County, CA) and its surrounding landscape have undergone considerable land reclamation and development since the mid-nineteenth century.

Lower Walnut Creek (Contra Costa County, CA) and its surrounding landscape have undergone considerable land reclamation and development since the mid-nineteenth century. In 1965, the lower 22 miles of Walnut Creek and the lower reaches of major tributaries were converted to flood control channels to protect the surrounding developed land. In the recent past, sediment was periodically removed from the lower Walnut Creek Flood Control Channel to provide flow capacity and necessary flood protection. Due to the wildlife impacts and costs associated with this practice, the Contra Costa County Flood Control and Water Conservation District (District) is now seeking a new channel management approach that works with natural processes and benefits people and wildlife in a cost-effective manner. Flood Control 2.0 project scientists and a Regional Science Advisory Team (RSAT) worked with the District to develop a long-term management Vision for lower Walnut Creek that could result in a multi-benefit landscape that restores lost habitat and is resilient under a changing climate. Development of the Vision began with technical analyses focused on understanding past and present landscape functioning and the changes to key processes and landscape features over the past 150 to 200 years. The key findings from these analyses include the following: • Landscape change – During the mid-19th century, lower Walnut Creek was surrounded by a continuous expanse of tidal wetlands occupying approximately 5,000 acres. Perennial freshwater marsh, willow thicket, and alkali meadow formed a large non-tidal wetland complex that adjoined the tidal marsh on its southern end. Over the past century and a half, the non-tidal wetland complex has been lost completely and the tidal wetland area has decreased by 40%. The remaining marsh areas are highly fragmented and cut-off from Walnut Creek by engineered levees. The loss of tidal wetland area has resulted in a substantial decrease in tidal prism and contributed to current in-channel sediment accumulation issues. Around the mouth of Walnut Creek, sediment accumulation has caused the position of the shoreline to expand into the Bay by up to half a mile. • Sediment accumulation – Since 1965, approximately 1.4M cubic yards of sediment have been removed from lower Walnut Creek, with approximately 70% coming from the tidal zone downstream of head of tide (i.e., the inland extent of tidal inundation at mean higher high water). Repeat channel cross-section surveys indicate that the channel quickly fills in with sediment following dredging events (due in large part to decreased tidal prism and associated channel scour capacity) and that the channel bed elevation is currently at or near “quasi-equilibrium.” A channel sediment budget for 1965-2007 indicates that approximately 80% of the watershed-derived sediment made it through lower Walnut Creek and out to the Bay, while the remaining 20% was likely deposited directly following channel construction and subsequent dredging events.