Better documentation and understanding of long-term temporal dynamics of nitrogen (N) and phosphorus (P) in watersheds is necessary to support effective water quality management, in part because studies have identified time lags between terrestrial nutrient balances and water quality. We present annual time series data from 1969 to 2012 for terrestrial N and P sources and monthly data from 1972 to 2013 for river N and P for the Willamette River Basin, Oregon, United States. Inputs to the watershed increased by factors of 3 for N and 1.2 for P. Synthetic fertilizer inputs increased in total and relative importance over time, while sewage inputs decreased. For N, increased fertilizer application was not matched by a proportionate increase in crop harvest; N use efficiency decreased from 69% to 38%. P use efficiency increased from 52% to 67%. As nutrient inputs to terrestrial systems increased, river concentrations and loads of total N, total P, and dissolved inorganic P decreased, and annual nutrient loads were strongly related to discharge. The N:P ratio of both sewage and fertilizer doubled over time but there was no similar trend in riverine export; river N:P concentrations declined dramatically during storms. River nutrient export over time was related to hydrology and waste discharge, with relatively little influence of watershed balances, suggesting that accumulation within soils or groundwater over time is mediating watershed export. Simply managing yearly nutrient balances is unlikely to improve water quality; rather, many factors must be considered, including soil and groundwater storage capacity, and gaseous loss pathways.