Drought conditions during the study period of January 1, 2009, to September 30, 2013, caused a reduction in surface-water releases from water-supply storage infrastructure of the Rio Grande Project, which led to changes in surface-water and groundwater (conjunctive) use in downstream agricultural alluvial valleys. Surface water and groundwater in the agriculturally dominated alluvial Rincon and Mesilla Valleys were investigated in this study to measure the influence of drought and subsequent change in conjunctive water use on quantity and quality of these water resources. In 2013, the U.S. Geological Survey, in cooperation with the New Mexico Environment Department and the New Mexico Interstate Stream Commission, began a study to (1) calculate dissolved-solids loads over the study period at streamgages in the study area where data are available, (2) assess the temporal variability of dissolved-solids loads at and between each streamgage where data are available, and (3) relate the spatiotemporal variability of shallow groundwater data (groundwater levels and quality) within the alluvial valleys of the study area to spatiotemporal variability of surface-water data over the study period. This assessment included the calculation of surface-water dissolved-solids loads at streamgages as well as a mass-balance approach to measure the change in salt load between these streamgages. Bimodal surface-water discharge data led to a temporally-dynamic volumetric definition of release and nonrelease seasons. Continuous surface-water discharge and water-quality data from three streamgages on the Rio Grande were used to calculate daily dissolved-solids loads over the study period, and the results were aggregated annually and seasonally. Results show the majority of dissolved-solids loading occurs during release season; however, decreased duration of the release season over the 5-year study period has resulted in a decrease of the total annual loads at each streamgage. Calculation of the change of salt loads using a mass-balance approach was applied between streamgages. Results from these calculations suggest differing responses to releases in the Rincon and Mesilla Valleys over the period of study; there is a decreasing sink of salt in the Rincon Valley whereas there is an increasing sink of salt in the Mesilla Valley. Daily groundwater-level and water-quality data from shallow wells within the two alluvial valleys show spatial heterogeneity of water quality over the study period. Mass-balance salt-loading trends during the study period are similar to previous trends during the 1950s drought as well as a wet period in the 1980s. The similarity of salt-loading trends from the 1950s, 1980s, and 2000s independent of the climate indicates salt loading in this hydrologic setting may be driven by water-use practices rather than a single climatic variable.