CONTRIBUTION NO. 842 JUNE 2018 Sediment Supply to San Francisco Bay, Water Years 1995 through 2016: Data, trends, and monitoring recommendations to support decisions about water quality, tidal wetlands, and resilience to sea level rise Prepared by United States Geological Survey David Schoellhamer and Mathieu Marineau San Francisco Estuary Institute Lester McKee, Sarah Pearce, Pete Kauhanen, Micha Salomon, Scott Dusterhoff, Letitia Grenier, and Philip Trowbridge SAN FRANCISCO ESTUARY INSTITUTE • CLEAN WATER PROGRAM/RMP • 4911 CENTRAL AVE., RICHMOND, CA • WWW.SFEI.ORG Sediment Supply to San Francisco Bay, Water Years 1995 through 2016: Data, trends, and monitoring recommendations to support decisions about water quality, tidal wetlands, and resilience to sea level rise Prepared By: David Schoellhamer and Mathieu Marineau United States Geological Survey Sacramento, CA Lester McKee, Sarah Pearce, Pete Kauhanen, Micha Salomon, Scott Dusterhoff, Letitia Grenier, and Philip Trowbridge San Francisco Estuary Institute Richmond, CA June 11, 2018 SFEI Contribution # 842 Recommended Citation: Schoellhamer, D., L. McKee, S. Pearce, P. Kauhanen, M. Salomon, S. Dusterhoff, L. Grenier, M. Marineau, and P. Trowbridge. 2018. Sediment Supply to San Francisco Bay, Water Years 1995 through 2016: Data, trends, and monitoring recommendations to support decisions about water quality, tidal wetlands, and resilience to sea level rise. Published by San Francisco Estuary Institute, Richmond, CA. SFEI Contribution Number 842. ii Contents Executive Summary ................................................................................................................. viii What are the magnitudes and sources of fine and coarse sediment transported to San Francisco Bay? ............................................................................................................. viii What are the present temporal trends of fine and coarse sediment supply to San Francisco Bay? ........................................................................................................ ix What are scenarios for future sediment supply to San Francisco Bay? .................................... x How can sediment monitoring be improved to fill data gaps and better provide information for resource managers? ............................................................................... xi 1. Introduction ................................................................................................................... 1 Motivation and Objectives ........................................................................................................ 1 Summary of Recent Regional Scale Projects on Sediment Supply to the Bay ......................... 2 2. Methods .......................................................................................................................... 5 Sediment Supply from the Delta ............................................................................................... 5 Sediment Supply from Bay Area Watersheds ......................................................................... 10 Sediment Transport Between Subembayments ....................................................................... 20 3. Results ........................................................................................................................... 22 Sediment Supply from the Delta ............................................................................................. 22 Sediment Supply from Bay Area Watersheds ......................................................................... 31 Sediment Transport Between Subembayments ....................................................................... 46 4. Discussion ..................................................................................................................... 50 What are the magnitudes and sources of fine and coarse sediment transported to San Francisco Bay? ....................................................................................................... 50 What are the present temporal trends of fine and coarse sediment supply to San Francisco Bay? ....................................................................................................... 56 What are scenarios for future sediment supply to San Francisco Bay? .................................. 61 How can sediment monitoring be improved to fill data gaps and better provide information for resource managers? .............................................................................. 63 5. References .................................................................................................................... 72 6. Appendix ...................................................................................................................... 78 iii Figures Figure 2.1. USGS suspended-sediment concentration monitoring stations in the Bay-Delta. ....... 6 Figure 2.2. Monitoring locations used for bedload computations. ................................................. 9 Figure 2.3. USGS stream gages in the San Francisco Bay Watershed. ........................................ 15 Figure 2.4. Sub-regional regression relations between peak discharge and suspended- sediment loads. .................................................................................................................. 16 Figure 3.1. Total annual discharge, suspended-sediment load, and mean suspended-sediment concentration (SSC) at Mallard Island for water years 1995-2016. ................................. 24 Figure 3.2. Double mass diagram for Mallard Island, water years 1995-2016. ........................... 25 Figure 3.3. Double mass diagram for the lower Sacramento River 9 km upstream from Mallard Island, water years 1976-2014. ........................................................................... 27 Figure 3.4. Proportional total sediment loads (top) and yields (bottom) by county in which discharge to the Bay is located. ......................................................................................... 40 Figure 3.5. Annual discharge, suspended-sediment load, and discharge-weighted mean SSC estimated for the small tributaries discharging to San Francisco Bay from the nine adjacent counties. .............................................................................................................. 42 Figure 3.6. Double mass diagram for six individual small tributaries. Different lines on the same plot indicate periods with continuous data that are separated by data gaps. ........... 45 Figure 3.7. Estimated seaward suspended-sediment flux at the Benicia Bridge for water years 2002-2016. ............................................................................................................... 48 Figure 3.8. Cumulative sediment deposition in Suisun Bay since October 1, 2001. Negative values indicate erosion. ..................................................................................................... 48 Figure 3.9. Suisun Bay deposition as a function of Delta outflow. Data are from Table 3.9. ...... 49 Figure 4.1. Net proportional total loads to the Bay from key large tributaries after accounting for storage and removal of sediment from flood control channels. .................................. 52 Figure 4.2. Suisun Bay deposition. 1867-1990 data are from Cappiella et al. (1999). ................. 61 Figure 4.3. Relative magnitudes of sources of sediment and estimated operating costs of selected monitoring activities. .......................................................................................... 71 iv Tables Table 3.1. Total annual discharge, suspended-sediment load, and mean suspended-sediment concentration at Mallard Island for water years 1995-2016. ............................................ 23 Table 3.2. Statistical comparison of lines fit to segments of the WY 1995-2016 double mass diagram from continuous data at Mallard Island (Figure 3.2). ......................................... 25 Table 3.3. Statistical comparison of lines fit to segments of the WY 1976-2014 double mass diagram from monthly data in the lower Sacramento River (Figure 3.3). ........................ 27 Table 3.4. Bedload estimates from downstream-most gages in the Delta at Sacramento River at Rio Vista (SRV) and San Joaquin at Jersey Point (SJJ) and mass of bed-material removed from mining and dredging operations between these gages and Mallard Island (MAL). ................................................................................................................... 29 Table 3.5. Bedload estimates from downstream-most gages in the Delta at Sacramento River at Rio Vista (SRV) and San Joaquin at Jersey Point (SJJ) and mass of bed-material removed from mining and dredging operations between these gages and Mallard Island (MAL). ................................................................................................................... 34 Table 3.6. Estimated bedload in units of metric tonnes (thousand t/yr) in key larger tributaries in the Bay Area as compared to the total regional estimate. ........................... 35 Table 3.7. Sediment storage and removal in the fluvial portions of larger small tributaries in metric tonnes (t) as compared to the sum of all available information for the region. ..... 36 Table 3.8. Summary of sediment loads (Million metric tonnes, Mt) entering the Bay at the head of tides from all small tributaries that drain to the Bay from the nine-county urbanized Bay Area.