Increases in nitrogen loading over the past several decades have led to widespread water quality impairments across the U.S. Elevated awareness of the influence of climate variability on nitrogen loading has led to several studies investigating future climate change impacts on water quality. However, it remains unclear whether long-term climate impacts can already be observed in the historical record. Here, we quantify long-term trends in total nitrogen loading over the period 1987-2012 across the contiguous U.S. and attribute these trends to long-term changes in nitrogen inputs and climatic variables. We find that annual precipitation, extreme springtime precipitation, and springtime temperature are key drivers of trends in historical loading in most regions. These decadal climate trends have either amplified or offset loading trends expected from nitrogen inputs alone. We also find that rising temperatures have been insufficient to offset precipitation-induced loading increases, suggesting that future increases in temperature under climate change may have limited potential to counteract loading increases expected as a result of anticipated changes in precipitation. This work demonstrates the important role of decadal climate variability in long-term nitrogen loading, emphasizing the need to consider climate change risks when designing and monitoring nutrient reduction programs.