San Francisco Estuary and Watershed Science

The stability of levees in the Sacramento-San Joaquin Delta is threatened by continued subsidence of Delta peat islands. Up to 6 meters of land-surface elevation has been lost in the 150 years since Delta marshes were leveed and drained, primarily from oxidation of peat soils. Flooding subsided peat islands halts peat oxidation by creating anoxic soils, but net accumulation of new material in restored wetlands is required to recover land-surface elevations. We investigated the subsidence reversal potential of two 3 hectare, permanently flooded, impounded wetlands re-established on a deeply subsided field on Twitchell Island. The shallower wetland (design water depth 25 cm) was almost completely colonized by dense emergent marsh vegetation within two years; whereas, the deeper wetland (design water depth 55 cm) which developed spatially variable depths as a result of heterogeneous colonization by emergent vegetation, still had some areas remaining as open water after nine years. Changes in land-surface elevation were quantified using repeated sedimentation-erosion table measurements. New material accumulating in the wetlands was sampled by coring.

Land-surface elevations increased by an average of 4 cm/yr in both wetlands from 1997 to 2006; however, the rates at different sites in the wetlands ranged from -0.5 to +9.2 cm/yr. Open water areas of the deeper wetland without emergent vegetation had the lowest rates of land-surface elevation gain. The greatest rates occurred in areas of the deeper wetland most isolated from the river water inlets, with dense stands of emergent marsh vegetation (tules and cattails). Vegetated areas of the deeper wetland in the transition zones between open water and mature emergent stands had intermediate rates of land-surface gain, as did the entire shallower wetland. These results suggest that the dominant component contributing to land-surface elevation gain in these wetlands was accumulation of organic matter, rather than mineral sediment, and that accumulation of organic matter in emergent marshes is strongly affected by hydrologic factors. Re-established, non-tidal wetlands with managed hydrology can produce significant increases in land-surface elevations, which can help to improve levee stability and protect subsided islands from future flooding.

The occurrence and potential effects of current-use pesticides are of concern in the San Francisco Estuary watershed but our understanding of the spatial and temporal distribution of contamination is limited. This paper summarizes almost two decades of historical data and uses it to describe our current knowledge of the processes controlling the occurrence of current-use pesticides in the watershed. Monitoring studies analyze fewer than half of the pesticides applied in the watershed and most of our knowledge is about inputs of dissolved pesticides in the upper watershed. The four major seasonal patterns of riverine inputs of pesticides to the estuary can be identified by usage and transport mechanism. Dormant spray insecticides applied to orchards and herbicides applied to a variety of crops are transported by rainfall during the winter. Alfalfa pesticides are detected following rainfall and irrigation return flow in the spring, and rice pesticides are detected following release of rice field water in the summer. Irrigation return flows transport a variety of herbicides during the summer. In addition, pesticides applied on Delta islands can cause elevated pesticide concentrations in localized areas. Although not as well characterized, urban creeks appear to have their own patterns of insecticide concentrations causing toxicity throughout most of the year. Current-use pesticides have also been detected on suspended and bed sediments throughout the watershed but limited data make it difficult to determine occurrence patterns. Data gaps include the lack of analysis of many pesticides (or degradates), changing pesticide use, limited information on pesticide transport within the Delta, and an incomplete understanding of the transport and persistence of sediment-associated pesticides. Future monitoring programs should be designed to address these data gaps.

A sample design-based procedure for estimating pre-adult and adult delta smelt abundance is described. Using data from midwater trawl surveys taken during the months of September, October, November, and December for the years 1990 through 2006 and estimates of size selectivity of the gear from a covered codend experiment, stratified random sample ratio estimates of delta smelt abundance were made per month. The estimation procedure is arguably an improvement over the dimensionless delta smelt indices that have been used historically in that (1) the volume sampled is used in a manner that leads to directly interpretable numbers and (2) standard errors are easily calculated. The estimates are quite imprecise, i.e., coefficients of variation in the range of 100\% occurred. The point estimates are highly correlated with the monthly indices, and conclusions on abundance declines are quite similar. However, both the estimates and indices may suffer from selection biases if the trawl samples are not representative of the true densities. Future work is needed in at least three areas: (1) gathering additional information to determine the validity of assumptions made, in particular determining the possible degree of selection bias; (2) developing procedures that utilize survey data gathered from earlier life history stages, such as larval surveys; (3) embedding a life-history model into the population estimation procedure.