This review assesses gaps in water quality modeling, emphasizing opportunities to improve next-generation models that are essential for managing water quality and are integral to meeting goals of scientific and management agencies. In particular, this paper identifies gaps in water quality modeling capabilities that, if addressed, could support assessments, projections, and evaluations of management alternatives to support ecosystem health and human beneficial use of water resources. It covers surface water and groundwater quality modeling, dealing with a broad suite of physical, biogeochemical, and anthropogenic drivers. Modeling capabilities for six constituents (or constituent categories) are explored: water temperature, salinity, nutrients, sediment, geogenic constituents, and contaminants of emerging concern. Each constituent was followed through the coupled atmospheric-hydrologic-human system, with prominent modeling gaps described for a diverse array of relevant inputs, processes, and human activities. Commonly identified modeling gaps primarily fall under three types: (1) model gaps, (2) data gaps, and (3) process understanding gaps. In addition to potential solutions for addressing specific individual modeling limitations, some broad approaches (e.g., enhanced data collection and compilation, machine learning, reduced-complexity modeling) are discussed as ways forward for tackling multiple gaps. This gap analysis establishes a framework of diverse approaches that may support improved process representation, scale, and accuracy of models for a wide range of water quality issues.

Droughts are frequent events in the western US, and can disrupt water supply and degrade water quality, challenging water management in the Sacramento–San Joaquin Delta. This chapter for the State of Bay–Delta Science report describes what drought means for the Delta, how drought is managed in the Delta, and how drought management has changed over time. Projections of future climate indicate the possibility of increased frequency and severity of droughts, which would increasingly affect California’s water system, society, and ecological functions within and beyond the Delta. California has experienced several major droughts in the 20th and 21st centuries, each of which has caused significant social and ecological effects, and has motivated improvements in water management. Droughts decrease native fish populations, increase harmful algal blooms, and promote the spread of many invasive plant and animal species. For people living within the Delta and those that rely on Delta water exports, droughts increase drinking water costs and decrease agricultural production, negatively affecting agricultural economies and labor markets. Tools developed in response to droughts include actions that increase supply (such as building water infrastructure), actions to reduce demand (such as water-conservation campaigns), and mitigation actions (such as monetary relief for drought-affected impacted communities. Improving drought resilience requires development of additional drought responses, increased forecasting accuracy, and increased awareness of effects on vulnerable communities and ecosystems. Even with development of additional management actions, strategies, and regulations, meeting the current levels of demand for water will likely be difficult. Drought conditions already cause conflict between human and environmental uses, and—with more extreme droughts possible in the future and projected increases in demand—providing for all users’ needs, even with major changes to water management in the Delta, will be challenging.

Climate projections and their effects have been evaluated in the San Francisco Estuary as part of the U.S. Geological Survey’s CASCaDE2 project. Understanding the ecological effects of climate change can help manage and maintain the ecological health and productivity of the San Francisco Estuary. In this study, we assessed downscaled air temperature data from 10 global climate models (GCMs) under two representative concentration pathway (RCP) trajectories for greenhouse gas concentrations for three regions of the San Francisco Estuary: Suisun and Grizzly Bays, Suisun marsh, and the Sacramento-San Joaquin Delta. We also used previously derived regression models to estimate future water temperatures at 16 locations in the upper San Francisco Estuary. We used a thermal regime approach to summarize water temperature projections to investigate changes to the thermal regime of the upper San Francisco Estuary and used the Delta Smelt (Hypomesus transpacificus) to demonstrate the impacts that a warming climate may have on the habitat needs of this fish species. Our results suggested there were no major differences in the extent of air temperature warming among the three regions. Annual average air temperatures were projected to increase approximately 2.0 and 4.7°C by the end of the century for the low and high RCP scenarios, respectively. We found timing, frequency, and magnitude metrics varied by period and RCP scenario, while duration and variability metrics varied by space for water temperature thermal regimes. For example, the spawning window for Delta Smelt (thermal regime duration metric) is projected to expand in the future, with spawning starting earlier for both RCP scenarios for most sites. Although our thermal regime analysis focused on the life history of Delta Smelt, similar approaches could be used to assess climate change threats to a wide array of native and invasive terrestrial and aquatic species found in San Francisco Estuary.

Many river systems within the Central Valley of California have been disconnected from their floodplains, hypothesized to be partially responsible for declining Chinook salmon populations ( Oncorhynchus tshawytscha ). The primary floodplain of the system, Yolo By‐Pass (known regionally as “Yolo Bypass”), offered an opportunity to examine whether improved connectivity between the floodplain and river could limit negative climate change effects on salmon populations. Specifically, the top of the floodplain (Fremont Weir) is being modified to provide Sacramento River Chinook salmon better access to floodplain rearing habitat. We estimated restoration effects on the Yolo By‐Pass flood regime now and under future climate scenarios using flow rating curves. Additionally, we used temperature and flow‐specific effects on Chinook salmon population dynamics within the Yolo By‐Pass and Sacramento River complex to describe how the restoration project and climate change may interact to affect juvenile Chinook salmon biomass production. Our results indicate that the Fremont Weir restoration project will extend the frequency, timing, and duration of Yolo By‐Pass flooding. Our production model indicates that the modification will result in greater salmon entrainment rates into the Yolo By‐Pass, where salmon growth rates, survival rates, and biomass production were higher when compared to the Sacramento River main stem. The project appears to benefit all regional runs of Chinook salmon, which should help support life history diversity. Our results suggest that the weir modification should benefit native fish from the Central Valley that use floodplain habitat and that these benefits may be resilient to challenges created by a changing climate.

Earth and Space Science Open Archive PosterOpen AccessYou are viewing the latest version by default [v2]When Models Talk: Integrated Human-Hydro-Terrestrial Modeling to Assess Delaware River Basin Water Resource Vulnerability to DroughtAuthorsHedeffEssaidiDAubreyDuggerJeniKeismanNancyBakerAdamBenthemJoelBlomquistKatherineCalvinXingyuanChenSalmeCookGalenGorskiAndrewHamiltonLivHerdmanAbigailJayeiDNoahKnowlesPMillyDianaPedrazaiDJasonPopeAndreasPreiniDPatrickReediDGregoryRouzeKevinSampsonWardSanfordGabrielSenayJaredSmithiDTerrySohliDCharulekaVaradharajanChrisVernoniDDavidYatesJacobZwartiDSee all authors Hedeff EssaidiDCorresponding Author• Submitting AuthorUS Geological SurveyiDhttps://orcid.org/0000-0003-0154-8628view email addressThe email was not providedcopy email addressAubrey DuggerNational Center for Atmospheric Researchview email addressThe email was not providedcopy email addressJeni KeismanU.S. Geological Surveyview email addressThe email was not providedcopy email addressNancy BakerUSGS Indiana Water Science Centerview email addressThe email was not providedcopy email addressAdam BenthemU.S. Geological Surveyview email addressThe email was not providedcopy email addressJoel BlomquistU.S. Geological Surveyview email addressThe email was not providedcopy email addressKatherine CalvinPacific Northwest National Laboratoryview email addressThe email was not providedcopy email addressXingyuan ChenPacific Northwest National Laboratoryview email addressThe email was not providedcopy email addressSalme CookUS Geological Survey Woods Hole Science Centerview email addressThe email was not providedcopy email addressGalen GorskiUS Geological Surveyview email addressThe email was not providedcopy email addressAndrew HamiltonCornell Universityview email addressThe email was not providedcopy email addressLiv HerdmanUSGS New York Water Science Centerview email addressThe email was not providedcopy email addressAbigail JayeiDNational Center for Atmospheric ResearchiDhttps://orcid.org/0000-0003-4909-0492view email addressThe email was not providedcopy email addressNoah KnowlesU.S. Geological Surveyview email addressThe email was not providedcopy email addressP MillyUSGS Water Mission Areaview email addressThe email was not providedcopy email addressDiana PedrazaiDUS Geological SurveyiDhttps://orcid.org/0000-0003-4483-8094view email addressThe email was not providedcopy email addressJason PopeUSGS Virginia Water Science Centerview email addressThe email was not providedcopy email addressAndreas PreiniDNational Center for Atmospheric ResearchiDhttps://orcid.org/0000-0001-6250-179Xview email addressThe email was not providedcopy email addressPatrick ReediDCornell UniversityiDhttps://orcid.org/0000-0002-7963-6102view email addressThe email was not providedcopy email addressGregory RouzeKBRInc.view email addressThe email was not providedcopy email addressKevin SampsonNational Center for Atmospheric Researchview email addressThe email was not providedcopy email addressWard SanfordUnited States Geological Survey (USGS)view email addressThe email was not providedcopy email addressGabriel SenayU.S. Geological Survey Earth Resources Observation and Science (EROS) Centerview email addressThe email was not providedcopy email addressJared SmithiDUS Geological SurveyiDhttps://orcid.org/0000-0003-3124-8255view email addressThe email was not providedcopy email addressTerry SohliDUSGS Earth Resources Observation and Science CenteriDhttps://orcid.org/0000-0002-9771-4231view email addressThe email was not providedcopy email addressCharuleka VaradharajanLawrence Berkeley National Laboratoryview email addressThe email was not providedcopy email addressChris VernoniDJoint Global Change Research InstituteiDhttps://orcid.org/0000-0002-3406-6214view email addressThe email was not providedcopy email addressDavid YatesNational Center for Atmospheric Researchview email addressThe email was not providedcopy email addressJacob ZwartiDUS Geological SurveyiDhttps://orcid.org/0000-0002-3870-405Xview email addressThe email was not providedcopy email address

Sedimentation and turbidity have effects on habitat suitability in the San Francisco Bay‐Delta (Bay‐Delta), concerning key species in the bay as well as the ability of the delta marshes to keep pace with sea level rise. A daily rainfall runoff and transport model of the Sacramento River Basin of northern California was developed to simulate streamflow and suspended sediment transport to the Bay‐Delta for the next century (water years, WY2010–2099). The model was calibrated to historical streamflow and sediment data and applied using 10 Global Climate Models with two representative concentration pathways (RCP) each for WY1980–2099 from the IPCC 5th Assessment Report. Results indicate average increases in peak streamflow of +58% and +66% for the RCP 4.5 and 8.5 ensembles, respectively, by mid‐century and +62 and +96% by end‐of‐century. Sediment loads increased by +39% and +69% by end‐of‐century. Suspended sediment concentrations (SSC) increased on average by +4.6% and +6.7% for RCP 4.5 and 8.5, respectively, by end‐of‐century. Individual scenario results varied, and statistically significant increasing trends of sediment loads to the Bay‐Delta were found for the RCP 4.5 and 8.5 ensembles and five individual scenarios. Increased suspended sediment loads may have negative effects such as contaminant transport but also have positive effects that help protect against sea level rise, increase turbidity and fish habitat, and sustain wetland habitats in the Bay‐Delta.

First posted July 19, 2018 For additional information, contact: National Research ProgramU.S. Geological Survey345 Middlefield RoadMenlo Park, CA 94025 Projections of managed flows from the Sacramento River/San Joaquin River watershed, California, into the San Francisco Bay and Sacramento-San Joaquin Delta under scenarios of future climate change are needed for evaluations of potential impacts on water supply and estuarine ecosystems. A new, multiple-model approach for achieving this is described. First, downscaled global climate model outputs are used to drive an existing Variable Infiltration Capacity/Variable Infiltration Capacity Routing (VIC/RVIC) model of Sacramento/San Joaquin hydrology, resulting in projections of daily, unimpaired flows throughout the watershed. A management model, Computational Assessments of Scenarios of Change for the Delta Ecosystem phase 2 (CASCaDE2) modified CalSim (C2-CalSim), uses these projections as inputs and produces monthly estimates of reservoir and other infrastructure operations and resulting downstream managed flows. A historical resampling algorithm, CASCaDE2 resampling algorithm (CRESPI), also uses the projected daily unimpaired flows, along with historical managed flows, to estimate the daily variability in managed flows throughout the watershed. The monthly and daily managed-flow estimates are combined in a way that preserves the multi-decadal variability and century-scale trends produced by the C2-CalSim model and the day-to-day variability produced by the CRESPI algorithm. The performance of the new modeling approach is evaluated at major inflows to the Bay-Delta estuary using multiple metrics and found to be satisfactory for the purposes of future scenario evaluation.

A linked modeling approach has been undertaken to understand the impacts of climate and infrastructure on aquatic ecology and water quality in the San Francisco Bay-Delta region. The Delft3D Flexible Mesh modeling suite is used in this effort for its 3D hydrodynamics, salinity, temperature and sediment dynamics, phytoplankton and water-quality coupling infrastructure, and linkage to a habitat suitability model. The hydrodynamic model component of the suite is D-Flow FM, a new 3D unstructured finite-volume model based on the Delft3D model. In this paper, D-Flow FM is applied to the San Francisco Bay-Delta to investigate tidal, seasonal and annual dynamics of water levels, river flows and salinity under historical environmental and infrastructural conditions. The model is driven by historical winds, tides, ocean salinity, and river flows, and includes federal, state, and local freshwater withdrawals, and regional gate and barrier operations. The model is calibrated over a 9-month period, and subsequently validated for water levels, flows, and 3D salinity dynamics over a 2 year period.Model performance was quantified using several model assessment metrics and visualized through target diagrams. These metrics indicate that the model accurately estimated water levels, flows, and salinity over wide-ranging tidal and fluvial conditions, and the model can be used to investigate detailed circulation and salinity patterns throughout the Bay-Delta. The hydrodynamics produced through this effort will be used to drive affiliated sediment, phytoplankton, and contaminant hindcast efforts and habitat suitability assessments for fish and bivalves. The modeling framework applied here will serve as a baseline to ultimately shed light on potential ecosystem change over the current century. (C) 2017 The Authors. Published by Elsevier Ltd.

Projections of meteorology downscaled from global climate model runs were used to drive a model of unimpaired hydrology of the Sacramento/San Joaquin watershed, which in turn drove models of operational responses and managed flows. Twenty daily climate change scenarios for water years 1980–2099 were evaluated with the goal of producing inflow boundary conditions for a watershed sediment model and for a hydrodynamical model of the San Francisco Bay‐Delta estuary. The resulting time series of meteorology, snowpack, unimpaired flow, reservoir storage, and managed flow were analyzed for century‐scale trends. In the Sacramento basin, which dominates Bay‐Delta inflows, all 20 scenarios portrayed warming trends (with a mean of 4.1 °C) and most had precipitation increases (with a mean increase of 9%). Sacramento basin snowpack water equivalent declined sharply (by 89%), which was associated with a major shift toward earlier unimpaired runoff timing (33% more flow arriving prior to 1 April). Sacramento basin reservoirs showed large declines in end‐of‐September storage. Water‐year averaged outflows increased for most scenarios for both unimpaired and impaired flows, and frequency of extremely high daily unimpaired and impaired flows increased (increases of 175% and 170%, respectively). Managed Delta inflows were projected to experience large increases in the wet season and declines in the dry season. Changes in management strategy and infrastructure can mitigate some of these changes, though to what degree is uncertain.

AbstractTrend tests, linear regression, and canonical correlation analysis were used to quantify changes in National Weather Service Cooperative Observer (COOP) snow depth data and derived quantities, precipitation, snowfall, and temperature over the study period 1950–2010. Despite widespread warming, historical trends in snowfall and snow depth are generally mixed owing to competing influences of trends in precipitation. Trends toward later snow-cover onset in the western half of the conterminous United States and earlier onset in the eastern half and a widespread trend toward earlier final meltoff of snow cover combined to produce trends toward shorter snow seasons in the eastern half of the United States and in the west and longer snow seasons in the Great Plains and southern Rockies. The annual total number of days with snow cover exhibited a widespread decline. Monthly trend patterns show the dominant influence of temperature trends on occurrence of snow cover in the warmer snow-season months and a c...

Changes in the position of the low salinity zone, a habitat suitability index, turbidity, and water temperature modeled from four 100-year scenarios of climate change were evaluated for possible effects on delta smelt Hypomesus transpacificus, which is endemic to the Sacramento–San Joaquin Delta. The persistence of delta smelt in much of its current habitat into the next century appears uncertain. By mid-century, the position of the low salinity zone in the fall and the habitat suitability index converged on values only observed during the worst droughts of the baseline period (1969–2000). Projected higher water temperatures would render waters historically inhabited by delta smelt near the confluence of the Sacramento and San Joaquin rivers largely uninhabitable. However, the scenarios of climate change are based on assumptions that require caution in the interpretation of the results. Projections like these provide managers with a useful tool for anticipating long-term challenges to managing fish populations and possibly adapting water management to ameliorate those challenges.

The levee system in California's Sacramento-San Joaquin Delta helps protect freshwater quality in a critical estuarine ecosystem that hosts substan- tial agricultural infrastructure and a large human population. We use space-based synthetic aperture radar interferometry (InSAR) to provide synoptic vertical land motion measurements of the Delta and levee system from 1995 to 2000. We find that Delta ground motion reflects seasonal hydrologic signals superimposed on average subsidence trends of 3 to 20 mm yr -1 . Because the measurements are insensi- tive to subsidence associated with peat thickness variations over Delta-island length scales, it is most likely that InSAR rates reflect underlying Quaternary sedimentary column compaction. We combine InSAR rates with sea-level rise scenarios to quantify 21st century levee overtopping potential. If left unmitigat- ed, it is likely that 50 to 100 years from now much of the levee system will subside below design thresholds.

BACKGROUND:Accumulating evidence shows that the planet is warming as a response to human emissions of greenhouse gases. Strategies of adaptation to climate change will require quantitative projections of how altered regional patterns of temperature, precipitation and sea level could cascade to provoke local impacts such as modified water supplies, increasing risks of coastal flooding, and growing challenges to sustainability of native species.METHODOLOGY/PRINCIPAL FINDINGS:We linked a series of models to investigate responses of California's San Francisco Estuary-Watershed (SFEW) system to two contrasting scenarios of climate change. Model outputs for scenarios of fast and moderate warming are presented as 2010-2099 projections of nine indicators of changing climate, hydrology and habitat quality. Trends of these indicators measure rates of: increasing air and water temperatures, salinity and sea level; decreasing precipitation, runoff, snowmelt contribution to runoff, and suspended sediment concentrations; and increasing frequency of extreme environmental conditions such as water temperatures and sea level beyond the ranges of historical observations.CONCLUSIONS/SIGNIFICANCE:Most of these environmental indicators change substantially over the 21(st) century, and many would present challenges to natural and managed systems. Adaptations to these changes will require flexible planning to cope with growing risks to humans and the challenges of meeting demands for fresh water and sustaining native biota. Programs of ecosystem rehabilitation and biodiversity conservation in coastal landscapes will be most likely to meet their objectives if they are designed from considerations that include: (1) an integrated perspective that river-estuary systems are influenced by effects of climate change operating on both watersheds and oceans; (2) varying sensitivity among environmental indicators to the uncertainty of future climates; (3) inevitability of biological community changes as responses to cumulative effects of climate change and other drivers of habitat transformations; and (4) anticipation and adaptation to the growing probability of ecosystem regime shifts.

An increase in the rate of sea level rise is one of the primary impacts of projected global climate change. To assess potential inundation associated with a continued acceleration of sea level rise, the highest resolution elevation data available were assembled from various sources and mosaicked to cover the land surfaces of the San Francisco Bay region. Next, to quantify extreme water levels throughout the bay, a hydrodynamic model of the San Francisco Estuary was driven by a projection of hourly water levels at the Presidio. This projection was based on a combination of climate model outputs, an empirical model, and observations, and incorporates astronomical, storm surge, El Nino, and long-term sea level rise influences. Based on the resulting data, maps of areas vulnerable to inundation were produced, corresponding to specific amounts of sea level rise and recurrence intervals, including tidal datums. These maps portray areas where inundation will likely be an increasing concern. In the North Bay, wetlands and some developed fill areas are at risk. In Central and South bays, a key feature is the landward periphery of developed areas that would be newly vulnerable to inundation. Nearly all municipalities adjacent to South Bay face this risk to some degree. For the bay as a whole, as early as mid-century under this scenario, the one-year peak event nearly equals the 100-year peak event in 2000. Maps of vulnerable areas are presented and some implications discussed. Results are available for interactive viewing and download at http://cascade.wr.usgs.gov/data/Task2b-SFBay.

xi 1.0 Introduction 1 2.0 Flood Mechanisms and Warming in the Sierra Nevada 3 2.1. Historical Floods 3 2.2. Rainfall-Runoff Contributing Areas 8 2.3. Rain on Snow 11 2.4. Antecedent Soil Moisture 13 2.5. Synchronous Springtime Snowmelt 14 3.0 Projections of Future Atmospheric-River Storms 14 4.0 Hydrologic Simulation Analysis of Sierra Nevadan Floods 29 4.1. Method 29 4.2. Simulations of Changing Flood Risks 31 4.2.1. Northern Sierra Nevada 31 4.2.2. Southern Sierra Nevada 38 4.3. Summary 41 5.0 Tides, Storm Surges, and Floods 42 6.0 Conclusions 46 7.0 References 48 8.0 Glossary 53