The Yaqui River Basin (YRB) is the most important wheat-producing region in Mexico. The main source of irrigation water in the Yaqui basin (over 80%) is surface water. Crop production sustainability is therefore closely linked to YRB streamflow and potentially to its sensitivity to climate variability and land use changes. We study the sensitivity of streamflow to land cover change resulting primarily from conversion of natural vegetation to unirrigated agriculture within the basin. We also examine how this sensitivity is influenced by midscale (North American Monsoon) and large-scale (El Niño–Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO)) climate regimes. Streamflow simulations using the variable Infiltration Capacity Model were performed in which current land use was altered incrementally within the three major subbasins of the YRB. In general, we found that the sensitivity of basin runoff to ENSO-and PDO-related variations in precipitation was much greater than to land cover–related changes and was highest during winter. Furthermore, climate and land cover runoff sensitivities appear to be related; in El Niño (generally wet) years the sensitivity of streamflow to land cover change can be four times higher than in La Niña (generally dry) years. The sensitivity of streamflow to PDO phase was smaller. Streamflow sensitivities to climate were the highest when PDO and ENSO were in phase. We conclude that climate variability exerts stronger controls on the surface hydrology than does land use change associated with the extensification of agriculture. For instance, flows in El Niño versus La Niña years differed by 76% in winter and 16% in summer, whereas maximum monthly (winter) flow changes were at most 4%.