Human activities within a watershed, such as agriculture, urbanization, and dam building, may affect the sediment yield from the watershed. Because the equilibrium geomorphic form of an estuary is dependent in part on the sediment supply from the watershed, anthropogenic activities within the watershed have the potential to affect estuary geomorphology. The Sacramento River drains the northern half of California’s Central Valley and is the primary source of sediment to San Francisco Bay. In this paper, it is shown that the delivery of suspended-sediment from the Sacramento River to San Francisco Bay has decreased by about one-half during the period 1957 to 2001. Many factors may be contributing to the trend in sediment yield, including the depletion of erodible sediment from hydraulic mining in the late 1800s, trapping of sediment in reservoirs, riverbank protection, altered land-uses (such as agriculture, grazing, urbanization, and logging), and levees. This finding has implications for planned tidal wetland restoration activities around San Francisco Bay, where an adequate sediment supply will be needed to build subsided areas to elevations typical of tidal wetlands as well as to keep pace with projected sea-level rise. In a broader context, the study underscores the need to address anthropogenic impacts on watershed sediment yield when considering actions such as restoration within downstream depositional areas.

Shallow subembayments respond differently than deep channels to physical forces acting in estuaries. The U.S. Geological Survey measured suspended-sediment concentrations at five locations in Honker Bay, a shallow subembayment of San Francisco Bay, and the adjacent channel to investigate the spatial and temporal differences between deep and shallow estuarine environments. During the first freshwater pulse of the wet season, the channel tended to transport suspended sediments through the system, whereas the shallow area acted as off-channel storage where deposition would likely occur. Following the freshwater pulse, suspended-sediment concentrations were greater in Honker Bay than in the adjacent deep channel, due to the larger supply of erodible sediment on the bed. However, the tidal variability of suspended-sediment concentrations in both Honker Bay and in the adjacent channel was greater after the freshwater pulse than before. During wind events, suspended-sediment concentrations in the channel were not affected; however, wind played a crucial role in the resuspension of sediments in the shallows. Despite wind-wave sediment resuspension in Honker Bay, tidally averaged suspended-sediment flux was controlled by the flood-dominated currents.

Sedimentation in the Sacramento–San Joaquin River Delta builds the Delta landscape, creates benthic and pelagic habitat, and transports sediment-associated contaminants. Here we present a conceptual model of sedimentation that includes submodels for river supply from the watershed to the Delta, regional transport within the Delta and seaward exchange, and local sedimentation in open water and marsh habitats. The model demonstrates feedback loops that affect the Delta ecosystem. Submerged and emergent marsh vegetation act as ecosystem engineers that can create a positive feedback loop by decreasing suspended sediment, increasing water column light, which in turn enables more vegetation. Sea-level rise in open water is partially countered by a negative feedback loop that increases deposition if there is a net decrease in hydrodynamic energy. Manipulation of regional sediment transport is probably the most feasible method to control suspended sediment and thus turbidity. The conceptual model is used to identify information gaps that need to be filled to develop an accurate sediment transport model.

Geomorphic evolution of estuarine habitats and landscapes over decadal timescales (>10 years) is sensitive to sediment supply from the watershed as well as estuarine hydrodynamics. Sediment supply to Suisun Bay, California is subject to natural as well as anthropogenic influence, beginning with the drastic input of sediment during the hydraulic mining period of the late 19th century. Today sediment supply is declining due to reduction of the hydraulic mining sediment pulse, reservoir storage, and land use practices. Future climate change, land use change, and sea level rise are some of the many factors that may alter sediment supply and threaten ecologically beneficial estuarine habitats. We have developed an estuarine geomorphic model based on a traditional tidal timescale hydrodynamic/sediment transport model, by idealizing boundary conditions, applying novel calibration procedures, and implementing a simplified time-stepping method. The Regional Oceanic Modeling System (ROMS) was developed for Suisun Bay, for the purpose of hindcasting historical geomorphic change and modeling future scenarios of geomorphic change. Seaward boundary conditions were idealized using tidal harmonic prediction for tidal stage and velocity, and a synthetic time-series for sediment concentrations was constructed by applying typical seasonal wind patterns and the spring-neap tidal signal. Calibration of these idealized boundary conditions and bed sediment parameters was accomplished using sediment flux data for the boundaries of Suisun Bay from water years 1997 and 2004. Calibrating to sediment fluxes guarantees that modeled net geomorphic change will not exceed the total supply of sediment from landward and seaward sources. The successful simulations of 1997 and 2004 allow for the development of a time-stepping method that reduces computational expense. The method involves simulating the two distinct sediment-transport seasons of Suisun Bay as month-long periods, then extrapolating the results of each compressed period for the entire season. Computational time for hindcasting and future scenario simulations is now reduced by 85% using this simplified method.

This paper, part of the collection of research comprising the State of Bay–Delta Science 2016, describes advances during the past decade in understanding flow dynamics and how water-quality constituents move within California’s Sacramento–San Joaquin River Delta (Delta). Water-quality constituents include salinity, heat, oxygen, nutrients, contaminants, organic particles, and inorganic particles. These constituents are affected by water diversions and other human manipulations of flow, and they greatly affect the quantity and quality of benthic, pelagic, and intertidal habitat in the Delta. The Pacific Ocean, the Central Valley watershed, human intervention, the atmosphere, and internal biogeochemical processes are all drivers of flow and transport in the Delta. These drivers provide a conceptual framework for presenting recent findings. The tremendous expansion of acoustic and optical instruments deployed in the Delta over the past decade has greatly improved our understanding of how tidal variability affects flow and transport. Sediment is increasingly viewed as a diminishing resource needed to sustain pelagic habitat and tidal marsh, especially as sea level rises. Connections among the watershed, Delta, and San Francisco Bay that have been quantified recently highlight that a landscape view of this system is needed, rather than consideration of each region in isolation. We discuss interactions of multiple drivers and information gaps.

Residence times of dissolved substances and sedimentation rates in tidal channels are affected by residual (tidally averaged) circulation patterns. One influence on these circulation patterns is the longitudinal density gradient. In most estuaries the longitudinal density gradient typically maintains a constant direction. However, a junction of tidal channels can create a local reversal (change in sign) of the density gradient. This can occur due to a difference in the phase of tidal currents in each channel. In San Francisco Bay, the phasing of the currents at the junction of Mare Island Strait and Carquinez Strait produces a local salinity minimum in Mare Island Strait. At the location of a local salinity minimum the longitudinal density gradient reverses direction. This paper presents four numerical models that were used to investigate the circulation caused by the salinity minimum: (1) A simple one-dimensional (1D) finite difference model demonstrates that a local salinity minimum is advected into Mare Island Strait from the junction with Carquinez Strait during flood tide. (2) A three-dimensional (3D) hydrodynamic finite element model is used to compute the tidally averaged circulation in a channel that contains a salinity minimum (a change in the sign of the longitudinal density gradient) and compares that to a channel that contains a longitudinal density gradient in a constant direction. The tidally averaged circulation produced by the salinity minimum is characterized by converging flow at the bed and diverging flow at the surface, whereas the circulation produced by the constant direction gradient is characterized by converging flow at the bed and downstream surface currents. These velocity fields are used to drive both a particle tracking and a sediment transport model. (3) A particle tracking model demonstrates a 30 percent increase in the residence time of neutrally buoyant particles transported through the salinity minimum, as compared to transport through a constant direction density gradient. (4) A sediment transport model demonstrates increased deposition at the near-bed null point of the salinity minimum, as compared to the constant direction gradient null point. These results are corroborated by historically noted large sedimentation rates and a local maximum of selenium accumulation in clams at the null point in Mare Island Strait.

In this paper, we report on the adaptation and application of a one-dimensional marsh surface elevation model, the Wetland Accretion Rate Model of Ecosystem Resilience (WARMER), to explore the conditions that lead to sustainable tidal freshwater marshes in the Sacramento–San Joaquin Delta. We defined marsh accretion parameters to encapsulate the range of observed values over historic and modern time-scales based on measurements from four marshes in high and low energy fluvial environments as well as possible future trends in sediment supply and mean sea level. A sensitivity analysis of 450 simulations was conducted encompassing a range of porosity values, initial elevations, organic and inorganic matter accumulation rates, and sea-level rise rates. For the range of inputs considered, the magnitude of SLR over the next century was the primary driver of marsh surface elevation change. Sediment supply was the secondary control. More than 84% of the scenarios resulted in sustainable marshes with 88 cm of SLR by 2100, but only 32% and 11% of the scenarios resulted in surviving marshes when SLR was increased to 133 cm and 179 cm, respectively. Marshes situated in high-energy zones were marginally more resilient than those in low-energy zones because of their higher inorganic sediment supply. Overall, the results from this modeling exercise suggest that marshes at the upstream reaches of the Delta—where SLR may be attenuated—and high energy marshes along major channels with high inorganic sediment accumulation rates will be more resilient to global SLR in excess of 88 cm over the next century than their downstream and low-energy counterparts. However, considerable uncertainties exist in the projected rates of sea-level rise and sediment avail-ability. In addition, more research is needed to constrain future rates of aboveground and belowground plant productivity under increased CO₂ concentrations and flooding.