Ecological forecasts for marine resource management during climate extremes

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

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 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 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.

Ecologically Functional Floodplains: Connectivity, Flow Regime, and Scale

American Water Resources Association (AWRA) | March 31st, 2010

This paper proposes a conceptual model that captures key attributes of ecologically functional floodplains, encompassing three basic elements: (1) hydrologic connectivity

This paper proposes a conceptual model that captures key attributes of ecologically functional floodplains, encompassing three basic elements: (1) hydrologic connectivity between the river and the floodplain, (2) a variable hydrograph that reflects seasonal precipitation patterns and retains a range of both high and low flow events, and (3) sufficient spatial scale to encompass dynamic processes and for floodplain benefits to accrue to a meaningful level. Although floodplains support high levels of biodiversity and some of the most productive ecosystems on Earth, they are also among the most converted and threatened ecosystems and therefore have recently become the focus of conservation and restoration programs across the United States and globally. These efforts seek to conserve or restore complex, highly variable ecosystems and often must simultaneously address both land and water management. Thus, such efforts must overcome considerable scientific, technical, and socioeconomic challenges. In addition to proposing a scientific conceptual model, this paper also includes three case studies that illustrate methods for addressing these technical and socioeconomic challenges within projects that seek to promote ecologically functional floodplains through river‐floodplain reconnection and/or restoration of key components of hydrological variability.

Ecosystem variability along the estuarine salinity gradient: Examples from long-term study of San Francisco Bay

Limnology and Oceanography (Wiley) | March 25th, 2017

The salinity gradient of estuaries plays a unique and fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes. We use

The salinity gradient of estuaries plays a unique and fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes. We use variability along the salinity gradient of San Francisco Bay to illustrate some lessons about the diversity of spatial structures in estuaries and their variability over time. Spatial patterns of dissolved constituents (e.g., silicate) can be linear or nonlinear, depending on the relative importance of river-ocean mixing and internal sinks (diatom uptake). Particles have different spatial patterns because they accumulate in estuarine turbidity maxima formed by the combination of sinking and estuarine circulation. Some constituents have weak or no mean spatial structure along the salinity gradient, reflecting spatially distributed sources along the estuary (nitrate) or atmospheric exchanges that buffer spatial variability of ecosystem metabolism (dissolved oxygen). The density difference between freshwater and seawater establishes stratification in estuaries stronger than the thermal stratification of lakes and oceans. Stratification is strongest around the center of the salinity gradient and when river discharge is high. Spatial distributions of motile organisms are shaped by species-specific adaptations to different salinity ranges (shrimp) and by behavioral responses to environmental variability (northern anchovy). Estuarine spatial patterns change over time scales of events (intrusions of upwelled ocean water), seasons (river inflow), years (annual weather anomalies), and between eras separated by ecosystem disturbances (a species introduction). Each of these lessons is a piece in the puzzle of how estuarine ecosystems are structured and how they differ from the river and ocean ecosystems they bridge.

Effects Analysis for the Delta Smelt Fall Habitat Action in 2019

U.S. Bureau of Reclamation (USBR) | August 1st, 2019

Effects of Groundwater Pumping on Agricultural Drains in the Tule Lake Subbasin, Oregon and California

U.S. Geological Survey (USGS) | July 24th, 2015

Since 2001, irrigators in the upper Klamath Basin have increasingly turned to groundwater to compensate for reductions in surface-water allocation caused by shifts from

Since 2001, irrigators in the upper Klamath Basin have increasingly turned to groundwater to compensate for reductions in surface-water allocation caused by shifts from irrigation use to instream flows for Endangered Species Act listed fishes. The largest increase in groundwater pumping has been in and around the Bureau of Reclamation’s Klamath Irrigation Project, which includes the Tule Lake subbasin in the southern part of the upper Klamath Basin. Agricultural drains on the Klamath Project are an important source of water for downstream irrigators and for the Tule Lake and Lower Klamath Lake National Wildlife Refuges. U.S. Geological Survey regional groundwater-flow model simulations and records of irrigation-return flow pumped from the Tule Lake subbasin into the adjacent Lower Klamath Lake subbasin have indicated that water-level declines from pumping may be causing decreased flow of shallow groundwater to agricultural drains. To better define the effect of increased pumping on drain flow and on the water balance of the groundwater system, the annual water volume pumped from drains in three subareas of the Tule Lake subbasin was estimated and a fine-grid, local groundwater model of the Tule Lake subbasin was constructed. Results of the agricultural-drain flow analysis indicate that groundwater discharge to drains has decreased such that flows in 2012 were approximately 32,400 acre-ft less than the 1997–2000 average flow. This decrease was concentrated in the northern and southeastern parts of the subbasin, which corresponds with the areas of greatest groundwater pumping. Model simulation results of the Tule Lake subbasin groundwater model indicate that increased supplemental pumping is the dominant stress to the groundwater system in the subbasin. Simulated supplemental pumping and decreased recharge from irrigation between 2000 and 2010 totaled 323,573 acre-ft, 234,800 acre-ft (73 percent) of which was from supplemental pumping. The response of the groundwater system to this change in stress included about 180,500 acre-ft (56 percent) of decreased groundwater discharge to drains and a 126,000 acre-ft (39 percent) reduction in aquifer storage. The remaining 5 percent came from reduced groundwater flow to other model boundaries, including the Lost River, the Tule Lake sumps, and interbasin flow.