Drought or near drought conditions persisted in California from 2012 through 2016, followed by a high precipitation year in 2017. Long-term water quality monitoring of two key river stations, the Sacramento River at Freeport and the San Joaquin River near Vernalis, located within the largely agricultural Central Valley, allow for an examination of pesticide concentrations and mass loading. Daily models were constructed using an estimation procedure that links mean daily streamflow with pesticide concentration monitoring and time. There were 13 different pesticides and three degradation products modeled, including herbicides, fungicides, and insecticides. Not all pesticides were detected at each river site. There were eight pesticides modeled for the Sacramento River and fourteen for the San Joaquin River. Collectively, there were 16 models for these two sites that showed decreasing trends, 5 with increasing, and 1 with no trend. Mass loads of the modeled compounds increased in 2017 because of the high river discharge. Most pesticides had measured or modeled concentrations that were below acute and chronic toxicity benchmarks. One exception was the neonicotinoid insecticide imidacloprid, which had an increasing trend in concentration with levels that exceeded chronic toxicity thresholds for invertebrates, especially after 2015. The use of some pesticides decreased during this period of time which partly explains the decreasing concentration trends. However, some pesticides had increased useage but with decreasing river concentration. The preponderance of negative trends in concentration of most pesticides suggested that lack of rainfall during the drought resulted in less transport from treated fields to the streams.