Sediment transport, streamflow, and climate change: long-term resilience of the Bay-Delta

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Sediment supply is important to the health of the Sacramento-San Joaquin River Delta and San Francisco Bay (Bay-Delta) ecosystem. Sediment eroded from upland source areas in the Sacramento and San Joaquin watersheds is transported through the rivers to the Bay-Delta where it is deposited in mudflats and tidal wetlands, which in turn helps protect against the effects of sea-level rise. Sediment deposits are also vital to the preservation of wetlands and habitat for wildlife such as birds and fish. Sediment supply from the Sacramento River has been declining since at least the mid-1950s, due to trapping of sediment in reservoirs and legacy effects of hydraulic mining, among other landscape disturbances. The future sediment supply to the Bay-Delta is primarily dependent on the future climate, as sediment supply is strongly dependent on peak river flows.

map of the Sacramento River basin

Location of Sacramento River Basin study area and model domain, including major dams and streamgages.  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. Public domain.

Coastal wetlands, including the Bay-Delta, are under direct and increasing threat from land use change pressures, from indirect impacts of upstream disruption to sediment supply, and from development pressures and rising sea level on the coastline (Syvitski et al., 2009). Sustainable management of coastal wetlands and marine ecosystems offer a wide range of ecosystem services, including shoreline protection, nutrient cycling, water quality maintenance, flood control, habitat for birds and other wildlife such as fish, and opportunities for recreation.  

Over the past several decades, the health of the Bay-Delta has been in decline (Healey et al., 2008) due to a reduction in water and sediment supply, invasive species, toxic pollutants, land use changes, levee systems in the Delta, and land subsidence from the draining of wetlands. Suspended sediment concentration (SSC) is an important estuarine health indicator (Achete et al., 2017), and sediment supply to the Bay-Delta, which is derived from the upstream watershed, has been declining over the past half-century (Stern et al., 2016; Wright & Schoellhamer, 2004). Anthropogenic and natural changes to the watershed can contribute to a decline or increase in sediment supply, which in turn impacts primary production, fish habitat conditions, contaminant transport, marshlands, and protection against sea level rise. 

Simulating Future Sediment Supply 

The future of sediment supply to the Bay-Delta is largely unknown. Future assessments using climate and management scenarios are imperative to help manage the Bay‐Delta through natural and anthropogenic changes in sediment supply. The Computational Assessments of Scenarios of Change for the Delta Ecosystem (CASCaDE II) project is composed of a diverse set of interconnected models (global climate models, hydrodynamic, operational, marsh accretion, contaminants, and biological) that work together to quantify effects of climate change and management on the overall health of the San Francisco Bay‐Delta ecosystem.  

As part of the CASCaDE II project, a daily rainfall, runoff, and transport model (Hydrological Simulation Program - FORTRAN (HSPF)) 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) using 20 future climate projections. While streamflow has clearly been affected by the anthropogenic development of the Sacramento River watershed, it is likely that a combination of other factors, such as hydraulic mining, dam construction (reservoir sedimentation), land use changes, agricultural practices, logging, and river engineering works (levees, navigation dredging, etc.), and changes in climate have had a greater influence on sediment supply than streamflow. Reservoir sedimentation has been determined to be one of the main factors in the decline in sediment supply over the recent decades (Wright & Schoellhamer, 2004). 


murky water body surrounded by green trees

Turbid waters in the Little Holland Tract area of the Sacramento-San Joaquin Bay Delta, California. Sediment suspended in the water column causes turbidity, which in turn affects light penetration, ecological productivity, and habitat quality. In the Delta, turbidity has declined in response to decreasing sediment supply from the Sacramento River, leading to clearer water with implications for native fish as well as the proliferation of non-native submerged aquatic vegetation. Turbid water is a natural phenomenon that occurs in rivers and estuaries.​​​​​​​ Public domain.

The simulated projections indicate increased peak streamflow and increased sediment supply to the Bay‐Delta which would aid in marsh accretion and bolster the resilience of marshes against sea level rise. Maintaining marshes longer into the century sustains the habitat of many native fish and bird species that could otherwise be lost. Tidal flats and beaches in the San Francisco Bay rely on a constant sediment supply to be sustained, and the threshold rate of sea level rise resistance is typically dependent on sediment availability (Kirwan & Megonigal, 2013). Some fish species depend on turbid waters to reduce the risk of predation, as well as potential increased deposition of spawning gravels with very high flow events. Excessive fine‐grained sediment can clog spawning gravels for salmon. Too much sediment increases light attenuation and could have adverse effects on benthic organisms and thus the rest of the food web in the Bay‐Delta. 

Projected water and sediment supply trends for the next 100 years will help resource and land managers prepare for the effects of climate change in a complex and highly managed estuarine system. 








Achete, F., Van der Wegen, M., Roelvink, J. A., & Jaffe, B. (2017). How can climate change and engineered water conveyance affect sediment dynamics in the San Francisco Bay‐Delta system? Climatic Change, 142(3–4), 375–389. 

Healey, M. C., Dettinger, M. D., & Norgaard, R. B. (2008). The state of Bay‐Delta Science, 2008 (pp. 174). Sacramento, CA: CALFED Science Program. 

Kirwan, M. L., & Megonigal, J. P. (2013). Tidal wetland stability in the face of human impacts and sea‐level rise. Nature, 504(7478), 53– 60. 

Stern, M. A., Flint, L. E., Minear, J., Flint, A. L., & Wright, S. A. (2016). Characterizing changes in streamflow and sediment supply in the Sacramento River basin, California, using hydrological simulation program—FORTRAN (HSPF). Water, 8(10) 432 p, 432. 

Syvitski, J. P. M., Kettner, A. J., Overeem, I., Hutton, E. W., Hannon, M. T., Brakenridge, G. R., Day, J., Vörösmarty, C., Saito, Y., Giosan, L., & Nicholls, R. J. (2009). Sinking deltas due to human activities. Nature Geoscience, 2(10), 681– 686.  

Wright, S. A., & Schoellhamer, D. H. (2004). Trends in the sediment yield of the Sacramento River, California, 1957–2001. San Francisco Estuary and Watershed Science, 2(2). 


bar graphs displaying results of simulated future changes in snowpack and precipitation

Percent change in peak precipitation days (>95th percentile) (top panel), April 1st snow water equivalent (mm) by end‐of‐century (2070–2099) (bottom panel) compared to historical baseline (1980–2009) for 10 models for representative concentration pathways (RCP) 4.5 and 8.5, and ensemble averages.

To assess potential future trends in streamflow and sediment supply, the calibrated Hydrological Simulation Program - FORTRAN (HSPF) model (Stern et al., 2016) was run using 20 future climate projections (scenarios) with varying air temperature and precipitation. These 20 scenarios consist of 10 global climate models; each run using two representative (greenhouse gas) concentration pathways (RCPs), RCP 4.5 and RCP 8.5. RCP 8.5 represents a future with very high global population, slow economic growth and a technological change, and a high dependence on fossil fuels (Riahi et al., 2011), and RCP 4.5 represents a future in which greenhouse gas emissions are partially mitigated through technological advances and policy changes (Thomson et al., 2011). Comparisons between each scenario's historical period (WY1980–2009) and the end-of-century 30-year period (WY2070–2099) were analyzed to quantify projected changes in climate. 

The global climate model results for the Sacramento River Basin indicate that 60% of scenarios projected increases in average precipitation, with a general model consensus of increased peak precipitation, and an all model consensus of increased temperatures, with varying magnitudes that broadly depend on RCP. In California, snow is the primary source of surface water storage, and the April 1st snowpack measurement is a vital metric of the potential water resources available through the dry summer months. In our model domain, which is below the major reservoirs, modeled April 1st snow water equivalent (SWE) in the Sacramento River basin decreased dramatically across all future scenarios by end‐of‐century and is consistent with other studies assessing changes in snowpack in the Sierra Nevada (Gergel et al., 2017; Rhoades et al., 2018; Thorne et al., 2015). 

Projected precipitation changes were the main driving mechanism for changes in the magnitude of modeled streamflow. Current climate projections indicate increases in precipitation frequency and intensity for the Sacramento River Basin, which leads to increased peak streamflow. To a lesser extent, air temperature influenced streamflow by increasing evapotranspiration decreasing SWE, and changing the timing of snowmelt. Seasonal changes in streamflow by end-of-century from the historical baseline are evident across all scenarios, which affects the timing of water resources, water quality, and water temperature through the end of the warm season.  

The changes in precipitation and air temperature had varying effects on flow, sediment, and suspended sediment concentration (SSC), and mean sediment loads were more sensitive to changes in climate than mean streamflow and SSC. 

2 graphs depicting simulating two representative concentration pathway scenarios

Total annual sediment load (million metric tons, Mt) for the Sacramento River at Freeport location, for representative concentration pathway (RCP) 4.5 scenarios (gray lines) with 30‐year running average for RCP 4.5 ensemble in blue (top panel) and RCP 8.5 scenarios (gray lines) and 30‐year running average for RCP 8.5 ensemble in red (bottom panel).

Significant consequences arise from either too much or too little sediment. Although we found statistically significant increases in five of the 20 scenarios and the RCP 4.5 and 8.5 ensembles, the nonsignificant trends of a leveling off or decline of sediment are also plausible outcomes. A leveling off or continued decline of sediment could significantly deteriorate the health and resiliency of the Bay‐Delta as the climate continues to change. Increases in the most intense and frequent storms and atmospheric rivers projected in most scenarios would generate an increased amount of runoff and sediment transport. Temperature increases lead to earlier snow melt and therefore create larger magnitude floods earlier in the wet season and thus higher sediment loads than previously experienced in the watershed. The risk of increased intense flooding imposes additional failure risk to the Bay‐Delta levees, dams, and other infrastructure components that are already in need of reinforcing and repair. Water quality may become an increased concern with higher sediment loads since sediment can transport contaminants such as pesticides, herbicides, nutrients, and mercury. 

Even with the many caveats and assumptions of the combined modeling approach described here, results of the scenarios can be useful to managers who need to plan for the middle- and long-term time scales. Projected increases in peak flows and sediment suggest a number of possible management actions, including floodplain restoration to capture sediment during peak events, increasing groundwater recharge to manage peak flows and prepare for droughts, and bolstering flood control structures. 



Gergel, D. R., Nijssen, B., Abatzoglou, J. T., Lettenmaier, D. P., & Stumbaugh, M. R. (2017). Effects of climate change on snowpack and fire potential in the western USA. Climatic Change, 141(2), 287– 299. 

Rhoades, A. M., Jones, A. D., & Ullrich, P. A. (2018). The changing character of the California Sierra Nevada as a natural reservoir. Geophysical Research Letters, 45, 13,008– 13,019. 

Riahi, K., Rao, S., Krey, V., Cho, C., Chirkov, V., Fischer, G., Kindermann, G., Nakicenovic, N., & Rafaj, P. (2011). RCP 8.5—A scenario of comparatively high greenhouse gas emissions. Climatic change, 109(1–2), 33. 

Stern, M. A., Flint, L. E., Minear, J., Flint, A. L., & Wright, S. A. (2016). Characterizing changes in streamflow and sediment supply in the Sacramento River basin, California, using hydrological simulation program—FORTRAN (HSPF). Water, 8(10) 432 p, 432. 

Thomson, A. M., Calvin, K. V., Smith, S. J., Kyle, G. P., Volke, A., Patel, P., Delgado‐Arias, S., Bond‐Lamberty, B., Wise, M. A., Clarke, L. E., & Edmonds, J. A. (2011). RCP4. 5: A pathway for stabilization of radiative forcing by 2100. Climatic change, 109(1‐2), 77. 

Thorne, J. H., Boynton, R. M., Flint, L. E., & Flint, A. L. (2015). The magnitude and spatial patterns of historical and future hydrologic change in California's watersheds. Ecosphere, 6(2), 1– 30.