San Francisco Estuary and Watershed Science

The Sacramento–San Joaquin Delta (the Delta) is located on the western edge of California’s Central Valley and is of critical ecological and economic importance. However, ecosystem alterations for human uses changed many of the Delta’s natural processes, and it is now considered in need of restoration. An approach was developed to evaluate and rank restoration actions in the Delta under the Ecosystem Restoration Program’s Delta Regional Ecosystem Restoration Implementation Plan (DRERIP). The DRERIP approach provides an explicit framework for evaluating restoration actions, using linked conceptual models, an action evaluation procedure, and a decision-support tool. Conceptual models allow scientists and managers to synthesize scientific information and make qualitative predictions about ecosystem function and restoration outcomes to guide and focus restoration efforts. The action evaluation procedure is a structured assessment of restoration actions. The procedure clearly describes actions to be evaluated, assesses the magnitude (importance and scale) and certainty of anticipated ecological outcomes, estimates degrees of worth (achieving intended outcomes) and risk (causing adverse consequences), evaluates the reversibility of the action, and identifies opportunities for learning. The values for worthiness, risk, reversibility, and learning opportunity are used in the decision- support tool to determine the fate of a proposed action. The decision-support tool is a structured decision tree that determines the disposition of an action: whether a restoration project should be discarded, revised with a different approach and re-evaluated, or implemented; and, if implemented, at what scale (targeted research, pilot project, or full implementation). The DRERIP approach provides managers with a valuable tool for restoration planning, and a foundation for integration with quantitative methods for a comprehensive ecosystem restoration plan.

Central Valley Chinook must pass through the San Francisco Estuary as juveniles and again as maturing adults. Much attention has been given to the effects on Chinook of management of the freshwater part of the estuary, and the Sacramento–San Joaquin Delta, and especially to the effects on Chinook of diversions of water from the Delta. Here, I review available information on juvenile Chinook in and around the estuary that seems most relevant to management of the estuary and of Chinook. Most naturally produced juvenile fall Chinook enter the estuary as small fish (<50 mm) that typically use tidal habitats, and anthropogenic changes in the Delta and around the bays have sharply reduced that habitat. Nevertheless, there is evidence that many surviving naturally produced fall Chinook leave fresh water at <55 mm length. Juvenile Chinook from other runs are older and larger when they enter the estuary, and probably pass through it more rapidly. Presumably, these have been less directly affected by loss of tidal habitat, but are also affected by degradation of the estuarine ecosystem. The effects of Delta diversions on Chinook vary strongly by run and river of origin; surprisingly few Sacramento River fall Chinook have been recovered at the diversions. Central Valley Chinook, especially fall Chinook, are strongly affected by hatchery culture that reduces juvenile life-history diversity, probably results in density-dependent mortality in the estuary, and presumably reduces fitness for natural reproduction. Hatchery culture diverts juvenile fall Chinook away from, and precludes for selection for, the life history trajectories followed by most naturally produced fish, to which more attention should be given.

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.

Floodplains are among the most biologically productive and diverse ecosystems on Earth and they provide significant benefits to society such as attenuation of floodwaters, groundwater recharge, filtration of nutrients and sediments, carbon sequestration, fisheries productivity and recreation.  However, floodplains are also among the most converted and threatened ecosystems.  Floodplain habitats in the Sacramento-San Joaquin Delta, and throughout California’s Central Valley, have been greatly reduced from their historic extent and key processes that create and maintain floodplains, such as flood flows and meander migration, have been greatly altered.  These widespread alterations to habitats and processes have lead to declines in many species’ populations in California’s Central Valley and Delta, creating challenges for both environmental and water management. To address these challenges numerous entities and programs are now focused on restoring floodplains and other Delta habitats.  This paper provides a conceptual model for floodplains that characterizes the key features and identifies the critical processes, drivers, and linkages that allow floodplains to produce a variety of functional outputs of management importance.  These outputs include: (1) the floodplain habitat mosaic, including riparian vegetation and its associated wildlife; (2) spawning and rearing habitat for native fish; and (3) food-web productivity that can support native fish on the floodplain as well as be exported to downstream ecosystems.  The model emphasizes that the production of these outputs from floodplains requires vertical and lateral hydrological connectivity across a broad range of flow conditions.  For example, long-duration flooding in the spring promotes native fish spawning and food-web productivity that benefits native species.