Surface-water samples were collected from the Sacramento and San Joaquin Rivers where they enter the Sacramento–San Joaquin Delta, and analyzed by the U.S. Geological Survey for a suite of 99 current-use pesticides and pesticide degradates. Samples were collected twice per month from May 2012 through July 2013 and from May 2012 through April 2013 at the Sacramento River at Freeport, and the San Joaquin River near Vernalis, respectively. Samples were analyzed by two separate laboratory methods by using gas chromatography with mass spectrometry or liquid chromatography with tandem mass spectrometry. Method detection limits ranged from 0.9 to 10.5 nanograms per liter (ng/L).

A total of 37 pesticides and degradates were detected in water samples collected during the study (18 herbicides, 11 fungicides, 7 insecticides, and 1 synergist). The most frequently detected pesticides overall were the herbicide hexazinone (detected in 100 percent of the samples); 3,4-dichloroaniline (97 percent), which is a degradate of the herbicides diuron and propanil; the fungicide azoxystrobin (83 percent); and the herbicides diuron (72 percent), simazine (66 percent), and metolachlor (64 percent). Insecticides were rarely detected during the study. Pesticide concentrations varied from below the method detection limits to 984 ng/L (hexazinone).

Twenty seven pesticides and (or) degradates were detected in Sacramento River samples, and the average number of pesticides per sample was six. The most frequently detected compounds in these samples were hexazinone (detected in 100 percent of samples), 3,4-dichloroaniline (97 percent), azoxystrobin (88 percent), diuron (56 percent), and simazine (50 percent). Pesticides with the highest detected maximum concentrations in Sacramento River samples included the herbicide clomazone (670 ng/L), azoxystrobin (368 ng/L), 3,4-dichloroaniline (364 ng/L), hexazinone (130 ng/L), and propanil (110 ng/L), and all but hexazinone are primarily associated with rice agriculture.

In addition to the twice monthly sampling, surface-water samples were collected from the Sacramento River on 5 consecutive days following a rainfall event in the Sacramento urban area. Samples collected following this event contained an average of 11 pesticides. The insecticides carbaryl, fipronil, and imidacloprid; the herbicide DCPA; and the fungicide imazalil were only detected in the Sacramento River during this storm-runoff event, and two detections of fipronil during this period exceeded the U.S. Environmental Protection Agency Aquatic Life Benchmark (11 ng/L) for chronic toxicity to invertebrates in freshwater.

In San Joaquin River samples, 26 pesticides and (or) degradates were detected, and the average number detected per sample was 9. The most frequently detected compounds in these samples were hexazinone and metolachlor (detected in 100 percent of samples); diuron (96 percent); the fungicide boscalid (96 percent); the degradates 3,4-dicloroaniline (92 percent) and NN-(3,4-Dichlorophenyl)-N’-methylurea (DCPMU; 83 percent); simazine (83 percent); and azoxystrobin (75 percent). The pesticides with the highest detected maximum concentrations were hexazinone (984 ng/L), diuron (695 ng/L), simazine (524 ng/L), the herbicide prometryn (155 ng/L), metolachlor (127 ng/L), boscalid (112 ng/L), DCPMU (111 ng/L), and the herbicide pendimethalin (108 ng/L).