San Francisco Estuary and Watershed Science

The Sacramento-San Joaquin Delta is in a state of inevitable transition. Physical and financial pressures are likely to transform parts of the Delta into open water within the next 100 years. Because flooded islands have different habitat, water quality, and hydrodynamic implications depending on location, depth, orientation, and other physical factors, the state may decide to intentionally flood one or more Delta islands in an effort to better manage the Delta’s ecosystem and valuable water supplies. This paper outlines three sets of near term actions the state would have to take to begin transitioning towards intentional island flooding, and discusses legal and political challenges to those actions. Several key findings include the following: (1) amendments to California’s water code and revisions to the Delta Land Use and Resource Management Plan may help the state ensure the legal authority to differentiate levee policies within the Delta; (2) permits for a first, experimental flooded island will likely require the State Water Resources Control Board to revise the Delta Water Quality Control Plan to allow for more short-term flexibility and deal with conflicting ecosystem and water supply uses; and (3) the state may want to prepare mitigation plans for private landowners on neighboring islands whose levees could face new threats of erosion and/or seepage from a nearby flooded island in order to avoid inverse condemnation lawsuits. If the state decides to shift its levee policies in the Delta, serious consideration will need to be given these and additional common, regulatory, statutory, and constitutional laws.

Restorationists commonly plant overstory and understory species simultaneously at the outset of restoration, but a mature forest canopy may be necessary to facilitate survival of light-intolerant understory species. We conducted two experiments in riparian forest restoration sites along the Sacramento River to determine whether: (1) introducing understory species is more successful at the beginning of restoration or after the canopy has developed; (2) canopy cover directly (via reduced light) or indirectly (by reducing non-native competition) facilitates survival of native understory species; and (3) seeding or planting seedlings of understory species is most effective. Seven native understory species were introduced as both seeds and seedlings into an experiment that manipulated canopy cover (open or canopy) and non-native grass competition (control or grass-specific herbicide). We conducted another experiment using shade cloth to directly test the effect of different light levels on seedling survival and growth of three species. Both experiments showed that four species (Aristolochia californica, Carex barbarae, Clematis ligusticifolia, and Vitis californica) had higher survival under low-light conditions (canopy or shade cloth). In contrast, three species (Artemisia douglasiana, Euthamia occidentalis and Rubus californica) had similar survival across open and canopy conditions. Cover of unplanted understory vegetation (mostly non-native) was much lower under the canopy than in open plots treated with grass-specific herbicide. Establishment from seed was generally low and highly variable. Our results suggest that to restore understory species in riparian forests in north–central California: light-intolerant understory species should be planted after canopy closure; canopy cover is more effective than grass-specific herbicide at reducing non-native understory cover; and planting seedlings is more successful than direct seeding.

While there is substantial information about the upstream migration of commercially and recreationally important fishes, relatively little is known about the upstream migration of small-bodied species, particularly through estuaries. In the San Francisco Estuary, there is a major need to understand the behavior of delta smelt Hypomesus transpacificus, a small pelagic fish listed under the state and federal endangered species acts. The spawning migration period may be critical as upstream movements can result in entrainment in water diversions. In general, delta smelt live in the low-salinity zone of the estuary and migrate upstream for spawning. During the fall pre-migration period, delta smelt remain primarily within the low-salinity zone in the western Sacramento–San Joaquin Delta and Suisun Bay. There were no significant upstream shifts of fish into fresher water during late fall, suggesting that delta smelt do not show pre-migration staging behavior. Following winter “first flush” flow events that appear to trigger migration, upstream movement rates are relatively rapid, averaging 3.6 km/d, a finding consistent with results from particle-tracking simulations, laboratory studies, and other fishes. Like some other native fishes, delta smelt apparently “hold” in upstream areas following migration; most do not spawn immediately. Overall, delta smelt fit the pattern of a diadromous species that is a seasonal reproductive migrant. Emerging data suggest that there is variability in the migration behavior of delta smelt, a pattern contrary to the reigning viewpoint that all smelt migrate in winter.

Climate warming is likely to challenge many current conceptions and regulatory policies, particularly for water management. A warmer climate is likely to hinder flood operations in California’s Sacramento Valley by decreasing snowpack storage and increasing the rain fraction of major storms. This work examines how a warmer climate would change flood peaks and volumes for nine major historical floods entering Shasta, Oroville, and New Bullards Bar reservoirs, using current flood flow forecast models and current flood operating rules. Shasta and Oroville have dynamic flood operation curves that accommodate many climate-warming scenarios. New Bullards Bar’s more static operating rule performs poorly for these conditions. Revisiting flood operating rules is an important adaptation for climate warming.

Water exports from California’s Sacramento–San Joaquin Delta are an environmental concern because they reduce net outflows of fresh water from the Delta, and can entrain fish and disrupt flows within the Delta. If exports were no longer pumped from within the Delta, the regulatory issue becomes one of maintaining appropriate flows into and out of the Delta. This paper presents the results of two sets of hydro-economic optimization modeling runs, which were developed to represent a range of modified Delta operations and their economic and operational effects on California’s water supply system. The first set of runs represents decreasing export capacity from the Delta. The second set increases minimum net Delta outflow (MNDO) requirements. The hydro-economic model seeks the least–cost statewide water management scheme for water supply, including a wide range of resources and water management options. Results show that reducing exports or increasing MNDO requirements increase annual average statewide water scarcity, scarcity costs, and operating costs (from greater use of desalination, wastewater recycling, water treatment, and pumping). Effects of reduced exports are especially concentrated in agricultural communities in the southern Central Valley because of their loss of access to overall water supply exports and their ability to transfer remaining water to southern California. Increased outflow requirements increase water scarcity and associated costs throughout California. For an equivalent amount of average Delta outflows, statewide costs increase more rapidly when exports alone are reduced than when minimum outflow requirements are increased and effects are more widely distributed statewide.