Ecological and human health impairments related to excess nitrogen (N) in streams and rivers remain widespread in the United States (U.S.) despite recent efforts to reduce N pollution. Many studies have quantified the relationship between N loads to streams in terms of N mass and N inputs to watersheds; however, N concentrations, rather than loads, are more closely related to impacts on human health and aquatic life. Additionally, concentrations, rather than loads, trigger regulatory responses. In this study, we examined how N concentrations are related to N inputs to watersheds (atmospheric deposition, synthetic fertilizer, manure applied to agricultural land, cultivated biological N fixation, and point sources), land cover characteristics, and stream network characteristics, including stream size and the extent of lakes and reservoirs. N concentration data were collected across the conterminous U.S. during the U.S. Environmental Protection Agency’s 2008–09 National Rivers and Streams Assessment (n = 1966). Median watershed N inputs were 15.7 kg N ha−1 yr−1. Atmospheric deposition accounted for over half the N inputs in 49% of watersheds, but watersheds with the highest N input rates were dominated by agriculture-related sources. Total N input to watersheds explained 42% and 38% of the variability in total N and dissolved inorganic N concentrations, respectively. Land cover characteristics were also important predictors, with wetland cover muting the effect of agricultural N inputs on N concentrations and riparian disturbance exacerbating it. In contrast, stream variables showed little correlation with N concentrations. This suggests that terrestrial factors that can be managed, such as agricultural N use practices and wetland or riparian areas, control the spatial variability in stream N concentrations across the conterminous U.S.