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New Life for Eroding Shorelines: Beach and Marsh Edge Change in the San Francisco Estuary

San Francisco Estuary Institute (SFEI) | April 1st, 2020

Summary

Wind, waves, storms, and changing water levels have reshaped shorelines for millennia and continue to do so today. The current shape of the San Francisco (SF) Estuary sho

Wind, waves, storms, and changing water levels have reshaped shorelines for millennia and continue to do so today. The current shape of the San Francisco (SF) Estuary shoreline is relatively new; 15,000 years ago, the California shoreline was west of the Farallon Islands and 140 meters below its current level (Cohen and Laws 1992, Malamud-Roam et al. 2007). By approximately 6,000 years ago (the end of the last glacial epoch), the sea had risen to nearly its present level and filled what is now San Francisco Bay, allowing marshes to form and maintain themselves (Atwater 1979). More recently, humans have changed the shape of the shoreline. During the 1850s, many marshes expanded extensively due to increased sediment supply from hydraulic mining in the Sierra Nevada (Gilbert 1917, Goals Project 1999). Diking, dredging, and filling of marshes for agricultural and urban development began in the late 19th century and continued through the first half of the 20th century. Today, humans continue to reshape the shoreline through continued diking, dredging and filling as well as restoration projects, urbanization of watersheds, ferry wakes, and many other means. The most wide-ranging impact of human activity on the shape of shorelines is global climate change caused by greenhouse gas emissions, which is accelerating the rate of sea level rise worldwide (OPC 2018). Sea level rise is likely to cause much more dramatic changes in the shape of shorelines than have been seen in recent centuries. The magnitude and pace of change will depend on the rate of sea level rise, existing shoreline conditions, and the ability of shorelines to adapt.

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Novato Creek Baylands Historical Ecology Study

San Francisco Estuary Institute (SFEI) | July 31st, 2015

Summary

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

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. 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 (fig. 1; Collins 1998, PWA 2002).

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On-farm flood capture could reduce groundwater overdraft in Kings River Basin

California Agriculture (UCANR) | November 16th, 2016

Summary

Chronic groundwater overdraft threatens agricultural sustainability in California’s Central Valley. Diverting flood flows onto farmland for groundwater rechar

Chronic groundwater overdraft threatens agricultural sustainability in California’s Central Valley. Diverting flood flows onto farmland for groundwater recharge offers an opportunity to help address this challenge. We studied the infiltration rate of floodwater diverted from the Kings River at a turnout upstream of the James Weir onto adjoining cropland; and calculated how much land would be necessary to capture the available floodwater, how much recharge of groundwater might be achieved, and the costs. The 1,000-acre pilot study included fields growing tomatoes, wine grapes, alfalfa and pistachios. Flood flows diverted onto vineyards infiltrated at an average rate of 2.5 inches per day under sustained flooding. At that relatively high infiltration rate, 10 acres are needed to capture one CFS of diverted flood flow. We considered these findings in the context of regional expansion. Based upon a 30-year record of Kings Basin surplus flood flows, we estimate 30,000 acres operated for on-farm flood recharge would have had the capacity to capture 80% of available flood flows and potentially offset overdraft rates in the Kings Basin. Costs of on-farm flood capture for this study were estimated at $36 per acre-foot, less than the cost for surface water storage and dedicated recharge basins.

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Patterns in the use of a restored California floodplain by native and alien fishes

University of California, Davis (UC Davis) | July 7th, 2007

Summary

Fishes were sampled on the restored floodplain of the Cosumnes River in Central California in order to determine patterns of floodplain use. The floodplain was sampled fo

Fishes were sampled on the restored floodplain of the Cosumnes River in Central California in order to determine patterns of floodplain use. The floodplain was sampled for seven years (1998-2002, 2004-2005) during the winter-spring flooding season. The fishes fell into five groups: (1) floodplain spawners, (2) river spawners, (3) floodplain foragers, (4) floodplain pond fishes, and (5) inadvertent users. Eight of the 18 abundant species were natives, while the rest were aliens. There was a consistent pattern of floodplain use, modified by timing and extent of flooding. The first fishes to appear were floodplain foragers, inadvertent users, and juvenile Chinook salmon (river spawners). Next were floodplain spawners, principally Sacramento splittail and common carp. At the end of the season, in ponds of residual water, non-native annual fishes, mainly inland silverside and western mosquitofish, became abundant. Adult spawners left when inflow decreased; their juveniles persisted as long as flood pulses kept water levels up and temperatures low. Juvenile splittail and carp quickly grew large enough to dominate floodplain fish samples, along with smaller numbers of juvenile Sacramento sucker and pikeminnow (river spawners). Such juveniles left the Relatively few fishes that used the floodplain for spawning or rearing became stranded, except late season alien fishes. Most alien fishes had resident populations in adjacent river, sloughs, and ditches and were not dependent on the floodplain for persistence. This indicates that Central Valley floodplains managed to favor native fishes should have the following characteristics: (1) extensive early season flooding, (2) complete drainage by the end of the flooding season, (3) few areas with permanent water, (4) a mosaic of physical habitats, (5) regular annual flooding but with high variability in flood regime.

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Pesticide Concentrations of Surface Water and Suspended Sediment in Yolo By-Pass and Cache Slough Complex, California, 2019–2021

U.S. Geological Survey (USGS) | July 9th, 2024

Summary

Managed flow pulses in the north Sacramento-San Joaquin Delta are an adaptive management tool used in efforts to enhance food availability in delta smelt (Hypomesus trans

Managed flow pulses in the north Sacramento-San Joaquin Delta are an adaptive management tool used in efforts to enhance food availability in delta smelt (Hypomesus transpacificus) habitat as part of the North Delta Food Subsidies Action. The California Department of Water Resources (DWR) monitors non-managed seasonal and local flow pulses and managed flow pulses from agricultural drainage or main stem Sacramento River water redirected through Yolo By-Pass. Augmented flow pulses are hypothesized to improve net positive flow during summer and fall in Yolo By-Pass and enhance plankton availability in delta smelt habitat in Cache Slough complex. However, flow pulses may also result in unintended negative effects of increased pesticides that are transported through Yolo By-Pass. Here, we evaluate pesticides in surface water and suspended sediment correlated with flow pulses in Yolo By-Pass during the 2019–21 calendar years. Surface-water and suspended-sediment samples were collected by DWR personnel. Water samples were analyzed at the U.S. Geological Survey Organic Chemistry Research Laboratory in Sacramento, California, for a suite of as many as 178 current-use pesticides and pesticide degradates using gas chromatography with mass spectrometry (GC/MS), gas chromatography with tandem mass spectrometry, and liquid chromatography with tandem mass spectrometry. Suspended sediments filtered from water samples were analyzed for a suite of as many as 173 current-use pesticides and pesticide degradates. There were 52 different current-use pesticides and pesticide degradates detected in water samples collected throughout the study. Concentrations ranged from below method detection limits to 4,070 nanograms per liter. Five different compounds in water samples were detected with concentrations above U.S. Environmental Protection Agency aquatic life benchmarks. In suspended-sediment samples collected throughout the study, eight different current-use pesticides and pesticide degradates were detected. Total pesticide concentrations were highest at surface-water sites in the northern end of Yolo By-Pass and decreased farther downstream during the same sampling events. Total pesticide concentrations generally were higher for most surface-water sites immediately before or during the managed flow pulse in 2019 versus after the flow pulse. Finally, mean total pesticide concentrations for each surface-water site generally were higher during all of 2019 than 2021, regardless of sampling period.

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Petaluma Valley Historical Hydrology and Ecology Study

San Francisco Estuary Institute (SFEI) | March 1st, 2018

Summary

This study examines the historical hydrology and ecology of the Petaluma River watershed prior to major Euro-American modification, and analyzes landscape changes over th

This study examines the historical hydrology and ecology of the Petaluma River watershed prior to major Euro-American modification, and analyzes landscape changes over the past two centuries. Synthesizing information from hundreds of archival documents, the research reconstructs the historical form and function of wetland, riparian, and aquatic habitats and stream channels throughout the watershed, providing insights into habitat extent and distribution, streamflow and sediment dynamics, vegetation composition, wildlife support, and landscape change. Findings from this research can be used to help set restoration targets and to prioritize multi-benefit opportunities to restore wildlife habitat, enhance flood protection, increase groundwater recharge, and improve sediment management. This Executive Summary highlights key findings from the study.

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Productive wetlands restored for carbon sequestration quickly become net CO2 sinks with site-level factors driving uptake variability

PLOS | March 25th, 2021

Summary

Inundated wetlands can potentially sequester substantial amounts of soil carbon (C) over the long-term because of slow decomposition and high primary productivity, partic

Inundated wetlands can potentially sequester substantial amounts of soil carbon (C) over the long-term because of slow decomposition and high primary productivity, particularly in climates with long growing seasons. Restoring such wetlands may provide one of several effective negative emission technologies to remove atmospheric CO2 and mitigate climate change. However, there remains considerable uncertainty whether these heterogeneous ecotones are consistent net C sinks and to what degree restoration and management methods affect C sequestration. Since wetland C dynamics are largely driven by climate, it is difficult to draw comparisons across regions. With many restored wetlands having different functional outcomes, we need to better understand the importance of site-specific conditions and how they change over time. We report on 21 site-years of C fluxes using eddy covariance measurements from five restored fresh to brackish wetlands in a Mediterranean climate. The wetlands ranged from 3 to 23 years after restoration and showed that several factors related to restoration methods and site conditions altered the magnitude of C sequestration by affecting vegetation cover and structure. Vegetation established within two years of re-flooding but followed different trajectories depending on design aspects, such as bathymetry-determined water levels, planting methods, and soil nutrients. A minimum of 55% vegetation cover was needed to become a net C sink, which most wetlands achieved once vegetation was established. Established wetlands had a high C sequestration efficiency (i.e. the ratio of net to gross ecosystem productivity) comparable to upland ecosystems but varied between years undergoing boom-bust growth cycles and C uptake strength was susceptible to disturbance events. We highlight the large C sequestration potential of productive inundated marshes, aided by restoration design and management targeted to maximise vegetation extent and minimise disturbance. These findings have important implications for wetland restoration, policy, and management practitioners.

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Promoting atmospheric-river and snowmelt fueled biogeomorphic processes by restoring river-floodplain connectivity in California’s Central Valley

Springer | April 30th, 2015

Summary

Potential biogeomorphic benefits from intentional levee breaks and weir overflow on the managed floodplain-river system of California’s Sacramento and San Joaquin River

Potential biogeomorphic benefits from intentional levee breaks and weir overflow on the managed floodplain-river system of California’s Sacramento and San Joaquin River watershed (Central Valley) are discussed here. Prior to the nineteenth century, the system was characterized by natural levees alongside complex multichanneled rivers and tributaries, and geomorphic processes such as channel migration and avulsion, typical in lowland floodplain-river systems globally, dominated. Today, the floodplain-river system has been heavily modified with infrastructure such as levee embankments that disconnect floodplains from channels and diminish key processes of floodplain-river ecology. Unintentional levee breaks in river systems where floodplains have been developed for agriculture or urban uses still occur regularly (in a quarter of twentieth century years) and are sometimes catastrophic. Floodplain inundation, erosion, and sedimentation, the dominant geomorphic processes that occur during unintentional levee breaks, are flood risks in such embanked river systems. Climate and flood variability still dictate the frequency of unintentional levee breaks despite many decades of engineering. Of particular consequence are the so-called atmospheric-river (AR) storms. Since 1951, 81 % of breaks have occurred as a result of AR storms and flooding, while most of the rest occurred during snowmelt floods. Intentional levee breaks or planned weir overflows that are designed for floodplain restoration can facilitate a return towards more natural and dynamic biogeomorphic processes. In areas where room for flood-driven geomorphic processes is available on floodplains, local sediment scour and deposition near a levee break promote topographic diversity that enhances vegetation establishment and floodplain habitat. This chapter summarizes our current understanding of climate processes and flood variability that govern unintentional levee breaks or weir overflow. We also review examples of alternative flood management approaches in the Central Valley that promote processes necessary to restore or sustain lowland floodplain biogeomorphology. Future climate-driven changes in flood regime, such as enhanced flooding during winter months or more frequent atmospheric rivers, could be accommodated by additional intentional levee breaks or planned weir overflow for restoration. Implementation of these alternatives could be used to improve restoration policy and management of floods in embanked river floodplains.

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Recharge Area Protection (Resource Management Strategy)

California Department of Water Resources (DWR) | July 29th, 2016

Summary

Recharge areas are those areas that provide the primary means of replenishing groundwater. Good natural recharge areas are those where good quality surface water is able

Recharge areas are those areas that provide the primary means of replenishing groundwater. Good natural recharge areas are those where good quality surface water is able to percolate through the sediments and rocks to the saturated zone which contains groundwater. If recharge areas cease to function properly, it will limit groundwater replenishment and/or groundwater quality for storage or use. Protection of recharge areas requires a number of actions based on two primary goals: (1) ensuring that areas suitable for recharge continue to be capable of adequate recharge rather than being covered by urban infrastructure, such as buildings and roads, and (2) preventing pollutants from entering groundwater to avoid expensive treatment that may be necessary prior to beneficial use. Protection of recharge areas is necessary to maintain the quantity and quality of groundwater in the aquifer. However, protecting recharge areas by itself does not provide a supply of water. Recharge areas are functioning properly when aquifer storage capacity is available, sufficient permeable surface is present, and the adequate supply of good quality water to recharge the aquifer is available. Protecting existing and potential recharge areas allows them to serve as valuable components of a conjunctive management and groundwater strategy.

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Reconciling fish and farms: Methods for managing California rice fields as salmon habitat

PLOS | February 24th, 2021

Summary

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the pa

Rearing habitat for juvenile Chinook Salmon (Oncorhynchus tshawytscha) in California, the southernmost portion of their range, has drastically declined throughout the past century. Recently, through cooperative agreements with diverse stakeholders, winter-flooded agricultural rice fields in California’s Central Valley have emerged as ecologically functioning floodplain rearing habitat for juvenile Chinook Salmon. From 2013 to 2016, we conducted a series of experiments examining methods to enhance habitat benefits for fall-run Chinook Salmon reared on winter-flooded rice fields in the Yolo Bypass, a modified floodplain managed for flood control, agriculture, and wildlife habitat in the Sacramento River Valley of California. Investigations included studying the effect of 1) post-harvest field substrate; 2) depth refugia; 3) duration of field drainage; and 4) duration of rearing occupancy on in-situ diet, growth and survival of juvenile salmon. Post-harvest substrate treatment had only a small effect on the lower trophic food web and an insignificant effect on growth rates or survival of rearing hatchery-origin, fall-run Chinook Salmon. Similarly, depth refugia, created by trenches dug to various depths, also had an insignificant effect on survival. Rapid field drainage yielded significantly higher survival compared to drainage methods drawn out over longer periods. A mortality of approximately one third was observed in the first week after fish were released in the floodplain. This initial mortality event was followed by high, stable survival rates for the remainder of the 6-week duration of floodplain rearing study. Across years, in-field survival ranged 7.4–61.6% and increased over the course of the experiments. Despite coinciding with the most extreme drought in California’s recorded history, which elevated water temperatures and reduced the regional extent of adjacent flooded habitats which concentrated avian predators, the adaptive research framework enabled incremental improvements in design to increase survival. Zooplankton (fish food) in the winter-flooded rice fields were 53-150x more abundant than those sampled concurrently in the adjacent Sacramento River channel. Correspondingly, observed somatic growth rates of juvenile hatchery-sourced fall-run Chinook Salmon stocked in rice fields were two to five times greater than concurrently and previously observed growth rates in the adjacent Sacramento River. The abundance of food resources and exceptionally high growth rates observed.

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