Agricultural pollutant runoff is a major source of water contamination in California's Sacramento River watershed where 8500 km2 of agricultural land influences water quality. The Soil and Water Assessment Tool (SWAT) hydrology, sediment, nitrate and pesticide transport components were assessed for the Sacramento River watershed. To represent flood conveyance in the area, the model was improved by implementing a flood routing algorithm. Sensitivity/uncertainty analyses and multi-objective calibration were incorporated into the model application for predicting streamflow, sediment, nitrate and pesticides (chlorpyrifos and diazinon) at multiple watershed sites from 1992 to 2008. Most of the observed data were within the 95% uncertainty interval, indicating that the SWAT simulations were capturing the uncertainties that existed, such as model simplification, observed data errors and lack of agricultural management data. The monthly Nash–Sutcliffe coefficients at the watershed outlet ranged from 0.48 to 0.82, indicating that the model was able to successfully predict streamflow and agricultural pollutant transport after calibration. Predicted sediment loads were highly correlated to streamflow, whereas nitrate, chlorpyrifos and diazinon were moderately correlated to streamflow. This indicates that timing of agricultural management operations plays a role in agricultural pollutant runoff. Best management practices, such as pesticide use limits during wet seasons, could improve water quality in the Sacramento River watershed. The calibrated model establishes a modelling framework for further studies of hydrology, water quality and ecosystem protection in the study area. Copyright © 2012 John Wiley & Sons, Ltd.