EcoAtlas: Enhancing Regional Capacity for Habitat Restoration Project Tracking, Assessment and Reporting

San Francisco Estuary Institute (SFEI) | July 1st, 2016

This project consolidates information from a variety of existing datasets to signicantLly expand the project tracking functionality in EcoAtlas to include hundreds of h

This project consolidates information from a variety of existing datasets to signicantLly expand the project tracking functionality in EcoAtlas to include hundreds of habitat protection, enhancement, and restoration projects throughout the Central Valley and San Francisco Bay-Delta regions. The Project Tracker database has been redesigned to better accommodate detailed project information such as acres of distinct habitat types, species benefitted, progress and status, and funding sources. Additional functionality was added to enhance visual displays and queries of the tabular and spatial project data. As new projects are developed and existing projects enter new phases, information can be expanded and updated through the new online data entry forms. Additional spatial data layers such as “Modern Delta Habitat Types” allow users to evaluate projects within the context of existing ecological resources and other landscape characteristics and uses. Additional data, querying and mapping functionality will allow for improved analyses of changes in habitat extent, landscape-scale conservation planning, evaluation of progress towards meeting conservation objectives, and partnership building. By providing the tools needed to track and analyze landscape change, we will improve our ability to strategically conserve important habitats in the future.

Ecological Condition Assessments of California’s Perennial Wadeable Streams (2000 through 2006)

California State Water Resources Control Board (SWRCB) | October 15th, 2007

The struggle to adequately monitor the condition of waterbodies with limited financial resources is a challenge faced by water resource agencies worldwide. For a resource

The struggle to adequately monitor the condition of waterbodies with limited financial resources is a challenge faced by water resource agencies worldwide. For a resource agency to adequately meet its obligations to monitor and assess the condition of its waterbodies it must provide information at both the site-specific scale and the scale of the entire resource. This dual obligation requires different monitoring strategies. Traditional targeted monitoring (in which site locations are selected to meet specific monitoring goals) is essential for answering many key water quality monitoring questions (e.g., what is the condition of specific sites, how do site conditions vary seasonally and annually, where are the best and worst sites, what are the primary water quality problems at specific sites, what are the effects of specific watershed activities and/or BMPs). Although this approach can generate much valuable water quality data, it is unable to provide information about the overall condition of large populations of resources (e.g., all streams, lakes or wetlands in a state) unless the monitoring entity is prepared to perform a complete census of the targeted resource. Site specific monitoring approaches are also unable to provide an objective context for interpreting the data they generate.  However, the perspective provided from this context is a necessary logical foundation for a sound monitoring program. In the US, the need for a broader context for interpreting the results of targeted monitoring data has driven the development of alternate sampling designs at both the state and federal level. To meet this need, the U.S. EPA established its Environmental Monitoring and Assessment Program (EMAP), a long term research program designed to develop the tools and techniques needed for cost-effectively answering the fundamental status and trends questions in the Clean Water Act. The EMAP studies are based on a probabilistic survey design in which each sampling location represents a known proportion of the total resource of interest (e.g., percent of total stream length) with known statistical confidence. This design permits the inference of resource conditions for large geographic regions with a relatively small investment in sampling (Ringold et al. 1996, Olsen et al. 1999, Stevens and Olsen 2004). After completing assessments of the condition of Eastern lakes and the condition of wadeable streams in the Middle-Atlantic states, the EPA initiated a similar assessment of streams in the western states (WEMAP), which included a high density of sites in California. For the first time in 2006, the state of California used data from a probability survey to derive the condition assessments of its perennial streams in its 305(b) report to the US EPA (Ode and Rehn 2005, California State Water Resources Control Board 2006). These reports were developed to meet California’s obligation to monitor its compliance with the goal of biotic integrity stipulated under Clean Water Act §305(b). Prior to these report, the ABL has presented results of the Southern Coastal California intensification area (Rehn and Ode 2004), Northern Coastal California intensification area (Rehn et al. 2005) as demonstration projects. As the EPA’s Western EMAP sampling effort ended in 2003, the EPA strongly encouraged western states to continue the EMAP monitoring approach in their own state monitoring programs. Two monitoring programs in the California State Water Resources Control Board, the recently established Surface Water Ambient Monitoring Program (SWAMP) and the Non-Point Source Program (NPS) expressed interest in probabilistic sampling. In concert with (and with funding from) their counterparts in the EPA Region 9 Non-point Source Programs and Office of Water, NPS and SWAMP developed the California Monitoring and Assessment Program (CMAP) to provide an additional four years of statewide probabilistic sampling to support continued ecological condition assessments. The study designs used for these condition assessments were developed by the EPA’s Office of Research and Development. Since the state and federal NPS programs brought a strong interest in the relationship between non-point source pollution sources and aquatic life use, the sampling design was adapted to include an explicit stratification by landuse/ landcover.

Ecological Condition Assessments of California’s Perennial Wadeable Streams: Highlights from the Surface Water Ambient Monitoring Program’s Perennial Streams Assessment (PSA ) (2000-2007)

California State Water Resources Control Board (SWRCB) | October 1st, 2011

Since 2000, California has conducted three successive probability surveys of its perennial streams and rivers, each with a focus on biological endpoints. These surveys ar

Since 2000, California has conducted three successive probability surveys of its perennial streams and rivers, each with a focus on biological endpoints. These surveys are now combined and are managed collectively by the Surface Water Ambient Monitoring Program (SWAMP) under its Perennial Streams Assessment (PSA) program. In 2010, SWAMP’s Perennial Streams Assessment (PSA) conducted the State Water Board’s eleventh continuous year of probability monitoring of perennial, wadeable streams. To date, the program has collected biological data (invertebrates, algae) and associated chemical and habitat data from approximately 850 probabilistic sites statewide. These surveys have produced a wealth of data that can and should be used to inform many decisions made by California’s water resource agencies. For example, the  assessments in the 2006 California Water Quality Assessment Report (Clean Water Act Section 305(b) Report) were based in large part on data from these surveys.  Data from these surveys were also used in the development of the 2010 Integrated Report. This report highlights some of the most significant results from the first eight years of PSA and demonstrates some ways that these data can go beyond 305(b) and 303(d) applications to improve California’s water quality programs. The results presented in this summary represent just a fraction of the potential uses of data generated by these ongoing surveys. As the data  et becomes more robust, it will continue to support multiple uses for years to come. This report is organized around four questions that were used to frame management objectives for the State Water Board’s Non-Point Source Program (NPS), a major partner in PSA’s development: 1. What is the condition of California’s streams? 2. Is stream condition changing over time? 3. What is the relative condition of streams draining agricultural, urban and forested regions? 4. Which stressors have the strongest associations with biological condition? Future SWAMP reports will highlight the application of PSA data to various State Water Board water quality programs, including links to regional monitoring objectives.

Ecological forecasts for marine resource management during climate extremes

Nature Portfolio (Springer Nature) | December 5th, 2023

Ecological Health in the Nation’s Streams, 1993–2005

U.S. Geological Survey (USGS) | July 2nd, 2013

This report summarizes a national assessment of the ecological health of streams done by the U.S. Geological Survey's (USGS) National Water-Quality Assessment Program (NA

This report summarizes a national assessment of the ecological health of streams done by the U.S. Geological Survey's (USGS) National Water-Quality Assessment Program (NAWQA). Healthy functioning stream ecosystems provide society with many benefits, including water purification, flood control, nutrient recycling, waste decomposition, fisheries, and aesthetics. The value to society of many of these benefits is substantial; for example, sportfishing in the United States generates an estimated annual economic output of $125 billion, including more than 1 million jobs (National Research Council, 2005; American Sportfishing Association, 2008). Continued monitoring and assessment of the Nation’s streams is needed to support informed decisions that will safeguard this important natural and economic resource. The quality of streams and rivers is often assessed with measures of the chemical or physical properties of water. However, a more comprehensive perspective is obtained if resident biological communities are also assessed. Guidelines to protect human health and aquatic life have been established for specific physical and chemical properties of water and have become useful yardsticks with which to assess water quality. Biological communities provide additional crucial information because they live within streams for weeks to years and therefore integrate through time the effects of changes to their chemical or physical environment. In addition, biological communities are a direct measure of stream health—an indicator of the ability of a stream to support aquatic life. Thus, the condition of biological communities, integrated with key physical and chemical properties, provides a comprehensive assessment of stream health.

Ecological implications of modeled hydrodynamic changes in the upper San Francisco Estuary

San Francisco Estuary Institute (SFEI) | May 2nd, 2016

Understanding how the pre-development upper San Francisco Estuary supported native wildlife is challenging because our current understanding of local wildlife ecology is

Understanding how the pre-development upper San Francisco Estuary supported native wildlife is challenging because our current understanding of local wildlife ecology is largely based on the profoundly altered modern landscape. This difficulty is compounded by the dynamic nature of the upper estuary’s aquatic habitats, which naturally experience tremendous temporal variability, largely due to the region’s Mediterranean climate. One approach to understanding how the system historically supported native wildlife is through a lens of landscape ecology (Whipple et al. 2012; SFEI-ASC 2014). This memorandum documents the first efforts to understand the landscape ecology of the upper estuary, comprising the Sacramento-San Joaquin River Delta and Suisun Bay, using a 3D hydrodynamic model of the pre-development system. By studying the pre-development landscape, we hope to gain insight into the deficiencies of the contemporary landscape and to help develop solutions for remedying these deficiencies. 

Ecological implications of modeled hydrodynamic changes in the upper San Francisco Estuary

San Francisco Estuary Institute (SFEI) | June 3rd, 2016

The physical and ecological environment of the upper San Francisco Estuary has been profoundly altered since the early 1800s. Recent efforts have utilized maps of the upp

The physical and ecological environment of the upper San Francisco Estuary has been profoundly altered since the early 1800s. Recent efforts have utilized maps of the upper estuary’s historical habitat types to infer associated changes in desired ecosystem processes and functions. The work presented in this memo builds on these previous efforts, but utilizes a new tool for evaluating change over time: a 3D hydrodynamic model of the pre-development estuary. This model was constructed by Resource Management Associates (RMA) using a new digital elevation model of the pre-development upper estuary generated by SFEI and UC Davis (UCD) and “natural” boundary flows calculated by the California Department of Water Resources (CDWR). Once completed and calibrated, the pre-development model was paired with a similar model of the contemporary system in order to analyze hydrodynamic changes in the upper estuary. These analyses are presented in a technical memorandum published by RMA (2015). This memorandum takes these analyses and considers the ecological implications of modeled changes (see the “Results” section). Hydrodynamic analyses include analyzing changes in tidal prism, isohaline positions, low-salinity zone habitat, channel velocity, and source water distribution. Key findings include: • (1) a decrease in temporal salinity variability: the variability in X2 position across wet and critically dry years has been reduced, which would be expected to decrease site-scale heterogeneity in tidal marsh plant communities, with potential implications for the diversity and metapopulation dynamics of marsh animals; • (2) an increase in X2 position due to changes in estuarine geometry: changes in the geometry of the upper estuary have increased the position of X2 by an average of 3.23 km, which means substantially more water is now required to maintain X2 at any one position. Impacts of geometry-driven changes in X2 on wildlife populations are hard to predict given uncertainties in the mechanisms driving correlations between X2 and species abundance, but are potentially sizeable; • (3) loss of low-velocity refugia in blind channels: in the pre-development simulations, average channel velocities are up to 520% higher in the mainstem channel than at the head of the adjacent blind channel. Since the majority of the upper estuary's blind channels have been diked and filled, loss of these habitats is expected to have significantly decreased low-velocity refugia for aquatic organisms (such as outmigrating chinook salmon) and has likely decreased the heterogeneity of aquatic habitat with respect to velocity at the landscape-scale; • (4) changes in source water distribution: preliminary model results suggest San Joaquin source water “signal” has been severely truncated, while Sacramento “signal” has been widely diffused, which could contribute to a decrease in the ability of migratory organisms (especially adult salmon) to navigate the Delta using source-water specific chemical cues (though improved model calibration in the upper reaches of the estuary is needed to draw firm conclusions).

Ecological Limits of Hydrologic Alteration: Environmental Flows for Regional Water Management

U.S. Environmental Protection Agency (EPA) | March 20th, 2008

Worldwide, water conflicts are escalating as cities, industries, agriculture, and energy producers compete for limited freshwater supplies. At the same time, there is a g

Worldwide, water conflicts are escalating as cities, industries, agriculture, and energy producers compete for limited freshwater supplies. At the same time, there is a growing awareness of the need to maintain adequate freshwater flows in rivers, lakes, floodplains, aquifers, and estuaries to sustain biodiversity and the many benefits derived from the healthy, functioning ecosystems upon which local communities and economies depend. Efficient, integrated water resource management systems help  governments provide for growing human populations while protecting and restoring healthy freshwater ecosystems. The integration of ecological considerations into water management has been hampered by the difficulty, cost, and time required for determining environmental flows -- the quantity, timing, and quality of water flows required to sustain freshwater and estuarine ecosystems and the human livelihoods and well-being that depend on these ecosystems.  Environmental flow assessments scientifically evaluate tradeoffs between alteration of natural water flow patterns by humans and consequent changes in ecological health.

Ecological Studies of the Sacramento-San Joaquin Estuary, A Decennial Report 1961-1971

California Department of Fish and Wildlife (CDFW) | June 15th, 1972

Ecological winners and losers of extreme drought in California

Nature Portfolio (Springer Nature) | August 20th, 2018

An unprecedented era of climatic volatility is altering ecosystems across our planet. The potential scale, pace and consequences of this global change have been m

An unprecedented era of climatic volatility is altering ecosystems across our planet. The potential scale, pace and consequences of this global change have been modelled extensively, yet little empirical research has quantified the impacts of extreme climate events on the composition of contemporary ecological communities. Here, we quantified the responses of 423 sympatric species of plants, arthropods, birds, reptiles and mammals to California’s drought of 2012–2015—the driest period in the past 1,200 years for this global biodiversity hotspot. Plants were most responsive to one-year water deficits, whereas vertebrates responded to longer-term deficits, and extended drought had the greatest impact on carnivorous animals. Locally rare species were more likely to increase in numbers and abundant species were more likely to decline in response to drought, and this negative density dependence was remarkably consistent across taxa and drought durations. Our system-wide analysis reveals that droughts indirectly promote the long-term persistence of rare species by stressing dominant species throughout the food web. These findings highlight processes that shape community structure in highly variable environments and provide insights into whole-community responses to modern climate volatility.