San Francisco Estuary and Watershed Science

Water quality impairment and land surface subsidence threaten the viability of the Sacramento–San Joaquin Delta (Delta), a critical component of California’s water conveyance system. Current-day irrigation drainage through Delta island peat soils affects drinking water treatment and is linked to mercury transport, potentially posing both ecological and public health concerns. To cost-effectively treat agricultural drainage water from subsided Delta islands to reduce the export of drinking Water Quality Constituents of Concern and mitigate land subsidence through accretion, we studied hybrid coagulation-treatment wetland systems, termed Chemically Enhanced Treatment Wetlands (CETWs). We provide cost estimates and design recommendations to aid broader implementation of this technology. Over a 20-year horizon using a Total Annualized Cost analysis, we estimate treatment costs of $602 to $747 per acre-foot (ac‑ft) water treated, and $36 to $70 per kg dissolved organic carbon (DOC) removed, depending upon source water DOC concentrations for a small 3-acre CETW system. For larger CETW systems scaled for island sizes of 3,500 to 14,000 acres, costs decrease to $108 to $239 per ac-ft water treated, and $11 to $14 per kg DOC removed. We estimated the footprints of CETW systems to be approximately 3% of the area being treated for 4-day hydraulic retention time (HRT) systems, but they would decrease to less than 1% for 1-day HRT systems. CETWs ultimately address several of the Delta’s key internal issues while keeping water treatment costs competitive with other currently available treatment technologies at similar scales on a per-carbon-removed basis. CETWs offer a reliable system to reduce out-going DOC and mercury loads, and they provide the additional benefit of sediment accretion. System costs and treatment efficacy depend significantly on inflow source water conditions, land availability, and other practical matters. To keep costs low and removal efficacy high, wetland design features will need site-specific evaluation.

In 2015, the fourth year of the recent drought, the California Department of Water Resources installed a rock barrier across False River west of Franks Tract to limit salt intrusion into the Delta at minimal cost in freshwater. This Barrier blocked flow in False River, greatly reducing landward salt transport by decreasing tidal dispersion in Franks Tract. We investigated some ecological consequences of the Barrier, examining its effects on water circulation and exchange, on distributions of submerged aquatic vegetation (SAV) and bivalves, and on phytoplankton and zooplankton. The Barrier allowed SAV to spread to areas of Franks Tract that previously had been clear. The distributions of bivalves (Potamocorbula and Corbicula) responded to the changes in salinity at time–scales of months for newly settled individuals, to 1 or more years for adults, but the Barrier’s effect was confounded with that of the drought. Nutrients, phytoplankton biomass, and a Microcystis abundance index showed little response to the Barrier. Transport of copepods — determined using output from a particle-tracking model — indicated some intermediate-scale reduction with the Barrier in place, but monitoring data did not show a larger-scale response in abundance. These studies were conducted separately and synthesized after the fact, and relied on reference conditions that were not always suitable for identifying the Barrier’s effects. If barriers are considered in the future, we rcommend a modest program of investigation to replicate study elements, and to ensure suitable reference conditions are available to allow barrier effects to be distinguished unambiguously from other sources of variability.

Chemical and toxicological testing in the Cache Slough complex (the slough) of the North Delta indicated the aquatic biota are exposed to a variety of wastewater-derived food additives, pharmaceuticals, and personal care products in highest concentration during dry periods, and many insecticides, herbicides and fungicides with peak concentrations after winter rains. The insecticide groups currently known to be of greatest toxicological concern are the pyrethroids and the fiproles (i.e., fipronil and its degradation products). After stormwater runoff enters the system via Ulatis Creek, both pesticide groups attained concentrations that posed a threat to aquatic life. When the commonly used testing species, Hyalella azteca, was placed in Cache Slough, toxicity — and, at times, near total mortality — was seen over at least an 8-km reach of Cache Slough that extended from the uppermost end almost to the junction with the Deep Water Ship Channel. Previous work over many years has shown similar results after other winter storms. However, when H. azteca that carried a mutation providing resistance to pyrethroid pesticides were also deployed in the slough, no ill effects were observed, which provided strong evidence that pyrethroids were responsible for toxicity to the non-resistant strain. Abundant resident H. azteca in Cache Slough carry any of four mutations that provide resistance to pyrethroids. They also carry a mutation that provides resistance to organophosphate pesticides, and likely carbamate pesticides as well. After many years of exposure, sensitive genotypes have been nearly eliminated from the system, and replaced by a population unaffected by many insecticides now in common use. We offer a variety of reasons why this shift to a population with mutant genotypes is of considerable concern, but also note that society has yet to fully consider the ecological and regulatory ramifications of the evolutionary attainment of pollutant resistance.

Stakeholder interests have spurred the reintroduction of the critically endangered populations of Chinook Salmon to tributaries upstream of Shasta Dam, in northern California. We released two groups of acoustically tagged, juvenile hatchery, late-fall Chinook Salmon to determine how juvenile salmon would distribute and survive. We measured travel times to Shasta Dam, and the number of fish that moved between locations within Shasta Reservoir. We used mark-recapture methods to determine detection and apparent survival probabilities of the tagged fish as they traveled through five reaches of the Sacramento River from the McCloud River to San Francisco Bay (~590 km) over the two 3-month observation periods. After our first (February) release of 262 tagged fish, 182 fish (70%) were detected at least once at the dam, 41 (16%) were detected at least once downstream of Shasta Dam, and 3 (1%) traveled as far as San Francisco Bay. After the second (November) release of 355 tagged fish, only 4 (1%) were detected at Shasta Dam. No fish were detected below Shasta Dam, so we could not estimate survival for this second release group. The first release of fish was fortuitously exposed to exceptionally high river flows and dam discharges, which may have contributed to the more distant downstream migration and detection of these fish — though other factors such as season, diploid versus triploid, and fish maturation and size may have also contributed to release differences. The reported fish travel times as well as detection and survival rates are the first estimates of juvenile salmon emigration from locations above Shasta Dam in more than 70 years. This information should help inform resource managers about how best to assess juvenile winter-run Chinook Salmon and assist in their reintroduction to watersheds upstream of Shasta Dam.

Liberty Island, California, is a historical freshwater tidal wetland that was converted to agricultural fields in the early 1900s. Liberty Island functioned as farmland until an accidental levee break flooded the area in 1997, inadvertently restoring tidal marsh hydrology. Since then, wetland vegetation has naturally recolonized part of the site. We conducted a seed bank assay at the site and found that despite a lack of germination or seedling recruitment at the site, the seed bank contained a diverse plant community, indicating that the site’s continuous flooding was likely suppressing germination. Additionally, the frequency of germinating seeds in the seed bank did not represent the dominant adult plant community. We conducted a cold stratification study to determine if this observed disparity could be explained by seed germination dynamics, and whether germination could be enhanced using a pre-germination cold exposure, particularly for species of concern for wetland restoration. The cold stratification study showed that longer durations of pre-germination cold enhanced germination in Schoenoplectus acutus, but reduced germination in Schoenoplectus californicus, and had no effect on Typha latifolia. Overall, germination of S. californicus and S. acutus was much lower than T. latifolia. Our findings suggest that seeding may not be an effective restoration technique for Schoenoplectus spp., and, to improve restoration techniques, further study is needed to more comprehensively understand the reproduction ecology of important marsh species.