In arable systems, large amounts of nutrients, particularly of nitrogen (N) and phosphorus (P), are not efficiently converted into harvestable products and are lost from agricultural systems, with negative consequences for agricultural productivity and the environment. These nutrient losses are mediated by hydroclimatic processes causing nutrient leaching and volatilization. We quantify over the period 1987-2012 how water availability through the evaporative ratio (actual evapotranspiration divided by precipitation) and irrigation, agricultural practices, and edaphic conditions jointly affect nutrient use efficiencies in 110 agricultural catchments in the United States. We consider N and P use efficiencies (nitrogen use efficiency [NUE] and phosphorous use efficiency [PUE]) defined as ratios of catchment-scale N and P in harvested products over their respective inputs, as well as the NUE/PUE ratio, as an indication of catchment-scale N and P imbalance. Both efficiencies increase through time because of changes in climate and agronomic practices. Setting all else at the median value of the data set, NUE and PUE increased with evaporative ratio by 0.5% and 0.2% when increasing the evaporative ratio by 20% and by 4.9% and 18.8% in the presence of irrigation. NUE was also higher in catchments where maize and soybean were dominant (increasing by 2.3% for a 20% increase in maize and soybean fractional area). Soil properties, represented by mineral soil texture and organic matter content, had only small effects on the efficiencies. Our results show that both climatic conditions and crop choice are important drivers of nutrient use efficiencies in agricultural catchments.