San Francisco Bay

Translating Science-Based Restoration Strategies into Spatially-Explicit Restoration Opportunities in the Delta (2018 Bay-Delta Science Conference Presentation)

San Francisco Estuary Institute (SFEI) | July 2nd, 2018

In a previous report titled “A Delta Renewed” we offered a collection of guidelines for science-based ecological restoration in the Sacramento-San Joaquin Delta that

In a previous report titled “A Delta Renewed” we offered a collection of guidelines for science-based ecological restoration in the Sacramento-San Joaquin Delta that emphasized restoring or emulating natural processes, anticipating future changes associated with climate change, establishing appropriate configurations of habitat types at the landscape scale, and utilizing a variety multi-benefit management strategies. In this talk, we present on our recent work to support regional restoration planning efforts by developing a repeatable process for using these guidelines to identify spatially-explicit restoration opportunities. The process is largely GIS-based and utilizes spatial data on existing land cover and conservation status, habitat configuration (including patch sizes and distances), surface elevations (including depth of subsidence), and future changes in tidal elevations associated with sea-level rise.  By distilling generalized guidelines into spatially-explicit opportunities, we hope to provide a practical tool for incorporating science into planning. To that end, these new methods are currently being piloted through planning efforts focused on the Central Delta Corridor and the McCormack Williamson Tract, and are also being used to assist with the quantification of ecological restoration potential in the Delta Plan Ecosystem Amendment.

Trapping of Suspended Sediment by Submerged Aquatic Vegetation in a Tidal Freshwater Region: Field Observations and Long-Term Trends

Estuaries and Coasts (Springer) | July 14th, 2020

Widespread invasion by non-native, submerged aquatic vegetation (SAV) may modify the sediment budget of an estuary, reducing the availability of inorganic sediment requir

Widespread invasion by non-native, submerged aquatic vegetation (SAV) may modify the sediment budget of an estuary, reducing the availability of inorganic sediment required by marshes to maintain their position in the tidal frame. The instantaneous trapping rate of suspended sediment in SAV patches in an estuary has not previously been quantified via field observations. In this study, flows of water and suspended sediment through patches of invasive SAV were measured at three tidally forced, freshwater sites, all located within the Sacramento-San Joaquin Delta in California. An acoustic Doppler current profiler deployed from a roving vessel provided velocity and backscatter data used to quantify fluxes of both water and suspended sediment. Sediment trapping efficiency, defined as instantaneous net trapped flux divided by incident flux, was positive in 24 of 29 cases, averaging + 5%. Coupled with 3 years of measured sediment flux data at one site, this suggests that trapping averages 3.7 kg m−2 year−1. This estimate compares favorably with the mean mass accumulation rate of 3.8 kg m−2 year−1 estimated from dated sediment cores collected at the study sites. Long-term measurements made upstream reveal a strong negative trend (− 1.8% year−1) in suspended sediment concentration, and intra-annual changes in both suspended sediment concentration and percent fines. The large footprint and high spatial density of invasive SAV coupled with declining sediment supply are diminishing downstream suspended sediment concentrations, potentially reducing the resiliency of marshes in the Delta and lower estuary to future sea-level rise.

Tree height explains mortality risk during an intense drought

Nature Portfolio (Springer Nature) | September 26th, 2019

Forest mortality is accelerating due to climate change and the largest trees may be at the greatest risk, threatening critical ecological, economic, and social be

Forest mortality is accelerating due to climate change and the largest trees may be at the greatest risk, threatening critical ecological, economic, and social benefits. Here, we combine high-resolution airborne LiDAR and optical data to track tree-level mortality rates for ~2 million trees in California over 8 years, showing that tree height is the strongest predictor of mortality during extreme drought. Large trees die at twice the rate of small trees and environmental gradients of temperature, water, and competition control the intensity of the height-mortality relationship. These findings suggest that future persistent drought may cause widespread mortality of the largest trees on Earth.

Trends in Fish and Invertebrate Populations of Suisun Marsh January 2017 - December 2017

University of California, Davis (UC Davis) | January 31st, 2019

Suisun Marsh, at the geographic center of the northern San Francisco Estuary, is important habitat for native and non-native fishes. The University of California, Davis,

Suisun Marsh, at the geographic center of the northern San Francisco Estuary, is important habitat for native and non-native fishes. The University of California, Davis, Suisun Marsh Fish Study, in partnership with the California Department of Water Resources (DWR), has systematically monitored the marsh's fish populations since January 1980. The study’s main purpose has been to determine environmental and anthropogenic factors affecting fish distribution and abundance. 

Twenty-first century hydroclimate: A continually changing baseline, with more frequent extremes

National Academy of Sciences (NAS) | March 14th, 2022

Variability in hydroclimate impacts natural and human systems worldwide. In particular, both decadal variability and extreme precipitation events have substantial effect

Variability in hydroclimate impacts natural and human systems worldwide. In particular, both decadal variability and extreme precipitation events have substantial effects and are anticipated to be strongly influenced by climate change. From a practical perspective, these impacts will be felt relative to the continuously evolving background climate. Removing the underlying forced trend is therefore necessary to assess the relative impacts, but to date, the small size of most climate-model ensembles has made it difficult to do this. Here we use an archive of large ensembles run under a high-emissions scenario to determine how decadal “megadrought” and “megapluvial” events—and shorter-term precipitation extremes—will vary relative to that changing baseline. When the trend is retained, mean state changes dominate: In fact, soil moisture changes are so large in some regions that conditions that would be considered a megadrought or pluvial event today are projected to become average. Time-of-emergence calculations suggest that in some regions including Europe and western North America, this shift may have already taken place and could be imminent elsewhere: Emergence of drought/pluvial conditions occurs over 61% of the global land surface (excluding Antarctica) by 2080. Relative to the changing baseline, megadrought-/megapluvial risk either will not change or is slightly reduced. However, the increased frequency and intensity of both extreme wet and dry precipitation events will likely present adaptation challenges beyond anything currently experienced. In many regions, resilience against future hazards will require adapting to an ever-changing “normal,” characterized by unprecedented aridification/wetting punctuated by more severe extremes.

Uncertainty in El Niño-like warming and California precipitation changes linked by the Interdecadal Pacific Oscillation

Nature Portfolio (Springer Nature) | November 10th, 2021

Marked uncertainty in California (CA) precipitation projections challenges their use in adaptation planning in the region already experiencing severe water stress. Under

Marked uncertainty in California (CA) precipitation projections challenges their use in adaptation planning in the region already experiencing severe water stress. Under global warming, a westerly jet extension in the North Pacific analogous to the El Niño-like teleconnection has been suggested as a key mechanism for CA winter precipitation changes. However, this teleconnection has not been reconciled with the well-known El Niño-like warming response or the controversial role of internal variability in the precipitation uncertainty. Here we find that internal variability contributes > 70% and > 50% of uncertainty in the CA precipitation changes and the El Niño-like warming, respectively, based on analysis of 318 climate simulations from several multi-model and large ensembles. The Interdecadal Pacific Oscillation plays a key role in each contribution and in connecting the two via the westerly jet extension. This unifying understanding of the role of internal variability in CA precipitation provides critical guidance for reducing and communicating uncertainty to inform adaptation planning.

Undelivered Water: Fulfilling the CVPIA promise to Central Valley refuges

U.S. Bureau of Reclamation (USBR) | November 3rd, 2009

The 1992 Central Valley Project Improvement Act transformed California’s federal water management system by providing fish and wildlife a co-equal priority with other u

The 1992 Central Valley Project Improvement Act transformed California’s federal water management system by providing fish and wildlife a co-equal priority with other uses. In so doing, the Act mandated that the federal government establish a program, now known as the Refuge Water Supply Program (RWSP), to manage, secure, and deliver a reliable, clean water supply to serve the wetland habitat needs of nineteen federal, state, and private wildlife refuges in California’s Central Valley. The refuges protect a significant portion of the last remaining 5 percent of the historic Central Valley wetlands and provide birds of the Pacific Flyway habitat during critical periods when no other wetlands habitat may be available. In response to a request from OMB, the Bureau of Reclamation and the Fish and Wildlife Service established an Independent Panel to evaluate the performance of the RWSP component of the Central Valley Project Improvement Act.

Understanding Microplastic Levels, Pathways, and Transport in the San Francisco Bay Region

San Francisco Estuary Institute (SFEI) | October 2nd, 2019

Microplastics (particles less than 5 mm) are ubiquitous and persistent pollutants in the ocean and a pervasive and preventable threat to the health of marine ec

Microplastics (particles less than 5 mm) are ubiquitous and persistent pollutants in the ocean and a pervasive and preventable threat to the health of marine ecosystems. Microplastics come in a wide variety of shapes, sizes, and plastic types, each with unique physical and chemical properties and toxicological impacts. Understanding the magnitude of the microplastics problem and determining the highest priorities for mitigation require accurate measures of microplastic occurrence in the environment and identification of likely sources. To develop critical baseline data and inform solutions, the San Francisco Estuary Institute and the 5 Gyres Institute have completed the first comprehensive regional study of microplastic pollution in a major estuary.

Underwater Videographic Observations of Domesticated Delta Smelt in Field Enclosures

U.S. Geological Survey (USGS) | May 24th, 2022

The delta smelt (Hypomesus transpacificus) is a small, euryhaline fish species endemic to the Sacramento–San Joaquin Delta; it is protected under the U.S. and Californi

The delta smelt (Hypomesus transpacificus) is a small, euryhaline fish species endemic to the Sacramento–San Joaquin Delta; it is protected under the U.S. and California Endangered Species Acts, and because of declines in population abundance, the delta smelt may be vulnerable to extinction. The California Department of Water Resources (DWR) is conducting studies to test the viability of using domesticated fish to supplement the wild population of delta smelt. These studies have focused on examining the health and survival of domesticated delta smelt placed inside enclosures (circular cages that are approximately 1.5 meters tall by 1 meter in diameter) into the wild. We completed two parts within this study using underwater cameras inside the enclosures to observe fish behavior and their responses to certain stimuli. In both parts of the study, delta smelt behaviors were broadly categorized into two basic categories: (1) normal and (2) alarm. Normal behavior was characterized as calm, non-polarized, and docile swimming behavior. Alarm behavior was characterized by sudden and rapid darting, polarized frantic swimming activity, and tighter schooling polarization of individuals. The first part of the study took place in a semi-controlled agricultural pond on the campus of the University of California, Davis. At this agricultural pond, we developed methods of observation and documented how fish behaved in response to enclosure disturbances associated with routine cleaning and service that is required during extended field deployments of the enclosures. We observed that delta smelt behavior changed from normal to alarm at the onset of an enclosure service and from alarm to normal within about 2 minutes after the service ended. The second part of the study was completed in cooperation with the DWR. In October 2019, DWR deployed three enclosures in the Sacramento River near Rio Vista, California. To monitor survival rate of delta smelt, DWR permitted us to deploy cameras in one enclosure to document the frequency and duration of alarm behaviors exhibited by delta smelt and the frequency, duration, and intensity of three types of disturbances: (1) noise generated from passing boats, (2) noise generated from the enclosure moving in response to wave energy, and (3) vertical movements of the enclosure generated from wave energy. Alarm behaviors averaged about 2 minutes in duration and occurred most frequently during the evening compared to midday or morning. Each disturbance variable exhibited substantial variability in duration and intensity and occurred least frequently during the morning and evening compared to midday. Alarm behaviors appeared to be most associated with high intensity enclosure noises and vertical movements; however, limited replicate samples prohibited developing a statistical relation. Alarm behaviors did not directly contribute to injury or mortality of individual delta smelt; however, indirect or sublethal effects of alarm behaviors were not examined.

Unintended consequences of using maps to communicate sea-level rise

Nature Portfolio (Springer Nature) | June 26th, 2024