Emergent hypotheses about causes of the pelagic organism decline in the Sacramento–San Joaquin Delta (Delta) indicate that a more complete understanding of the quality of water entering the Delta is needed. Less than half of all pesticides used in the Delta watershed are measured in samples collected for routine monitoring, and with new pesticides continually being registered for use, the concentrations of unmonitored pesticides in the Delta ecosystem are unknown. In response, a multi-year, cooperative effort to improve monitoring of mercury, nutrients, pathogens, and pesticides was begun by the Delta Regional Monitoring Program (RMP). In July 2015, the U.S. Geological Survey in cooperation with the Delta RMP began measuring concentrations of 154 pesticide compounds in monthly samples of surface water and suspended sediment collected at five major inputs to the Sacramento–San Joaquin Delta from July 2015 to June 2016. In addition to pesticide concentration measurements, field water-quality indicators (water temperature, specific conductance, dissolved oxygen, pH, and turbidity) were measured at each site and samples were collected for the analysis of dissolved organic carbon, dissolved copper, particulate organic carbon, particulate inorganic carbon, total particulate carbon, and total particulate nitrogen. Pesticide concentrations in particulates were measured in collected suspended-sediment samples by gas chromatography with mass spectrometry, whereas concentrations measured in surface-water samples utilized a combination of gas chromatography with mass spectrometry and liquid chromatography with tandem mass spectrometry. Samples were collected from two sites in the San Joaquin River watershed and at one site for each of the Mokelumne River, Sacramento River, and Ulatis Creek watersheds.

All water samples contained mixtures of 2–25 pesticides. Pesticides were detected in 100 percent of surface-water samples. A total of 54 pesticide compounds were detected in water samples during the study period (19 fungicides, 18 herbicides, 9 insecticides, 7 breakdown products, and 1 synergist). The most frequently detected pesticide compounds were the herbicides hexazinone (95 percent) and diuron (73 percent) and the fungicides boscalid (93 percent) and azoxystrobin (75 percent). Pesticide concentrations ranged from below the method detection limits to 2,630 nanograms per liter for the herbicide metolachlor.

A total of 11 pesticide compounds were detected in the suspended sediments filtered from water samples (6 herbicides, 3 insecticides, 1 fungicide, and 1 breakdown product). The most frequently detected compounds were the insecticides permethrin (7 percent) and bifenthrin (5 percent) and the herbicide pendimethalin (5 percent). Pesticide concentrations in the suspended-sediment ranged from below the method detection limit to 265 nanograms per liter for the herbicide pendimethalin.