Relationships between long-term data from the Fernow Experimental Forest (FEF) and historical records of precipitation, NOx (nitric oxide + nitrogen dioxide) emissions, and \(\delta\) 15N tree-ring data were used to reconstruct a 123-year history of atmospheric nitrogen (N) inputs and stream water N outputs for a small watershed in West Virginia. This long-term perspective revealed that baseline rates (1900–1910) of atmospheric N deposition and N losses in stream water were ~ 5 kg N/ha/yr and ~ 1.5 kg N/ha/yr, respectively. Anthropogenic NOx emissions and atmospheric N deposition exhibited a temporal pattern of increasing N deposition from 1900 until ca. 1974, followed by a nearly complete return to baseline levels beginning ca. 1997 and after amendments to the Clean Air Act in the United States. In contrast, there was no temporal synchrony between atmospheric N inputs and the flux of N into stream water. The discharge of N in stream water remained low from 1900 until ~ 1974 when it increased by 233% over a period of ten years once atmospheric inputs exceeded a critical load of ~ 16 kg N/ha/yr. Following the decline in N inputs below the critical load, stream water N losses remained high for ~ 10 years and then decreased 30% by 2023. Over the entire period, ~ 74% of cumulative N inputs were apparently retained in the watershed. Initially, N retention was ~ 80% but declined to ~ 45% by 2023. Important observations contained in the reconstructed > 100-year history at this location would have likely been missed over the much shorter time span of a typical research grant, underscoring the value of long-term environmental data in broadening our understanding of ecosystem behavior.