Surface-water samples were collected from sites within the Sacramento-San Joaquin Delta and Grizzly Bay, California, during the spring in 2011 and 2012, and they were analyzed by the U.S. Geological Survey for a suite of 99 current-use pesticides and pesticide degradates. Samples were collected and analyzed as part of a collaborative project studying the occurrence and characteristics of phytoplankton in the San Francisco Estuary. Samples were analyzed by two separate laboratory methods employing gas chromatography/mass spectrometry or liquid chromatography with tandem mass spectrometry. Method detection limits ranged from 0.9 to 10.5 nanograms per liter (ng/L). Eighteen pesticides were detected in samples collected during 2011, and the most frequently detected compounds were the herbicides clomazone, diuron, hexazinone and metolachlor, and the diuron degradates 3,4-dichloroaniline and N-(3,4-dichlorophenyl)-N’-methylurea (DCPMU). Concentrations for all compounds were less than 75 ng/L, except for the rice herbicide clomazone and the fungicide tetraconazole, which had maximum concentrations of 535 and 511 ng/L, respectively. In samples collected in 2012, a total of 16 pesticides were detected. The most frequently detected compounds were the fungicides azoxystrobin and boscalid and the herbicides diuron, hexazinone, metolachlor, and simazine. Maximum concentrations for all compounds detected in 2012 were less than 75 ng/L, except for the fungicide azoxystrobin and the herbicides hexazinone and simazine, which were detected at up to 188, 134, and 140 ng/L, respectively.