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There has been extensive analysis of Clean Air Act Amendment (CAAA) regulation impacts to changes in atmospheric nitrogen deposition; however, few studies have focused on watershed nitrogen transfer particularly regarding long-term predictions. In this study, we investigated impacts of CAAA NOx emissions on the fate and transport of nitrogen for two watersheds in the Neuse River Basin. We applied the Soil and Water Assessment Tool (SWAT) using simulated deposition rates from the Community Multiscale Air Quality (CMAQ) model. Two scenarios were investigated: one that considered CAAA emission controls in CMAQ simulation ( with) and a second that did not ( without). By 2020, results showed a 70 % drop in nitrogen discharge for the Little River watershed and a 50 % drop for the Nahunta watershed from 1990 levels under the with-CAAA scenario. Denitrification and plant nitrogen uptake played important roles in nitrogen discharge from each watershed. Nitrogen watershed response time to a change in atmospheric nitrogen deposition was 4 years for Nahunta and 2 years for Little River. We attribute these differences in nitrogen response time to contrasts in agricultural land use and diversity of crop types. Soybean, hay, and corn land covers had comparatively longer response times to changes in atmospheric deposition. The studied watersheds demonstrate relatively large nitrogen retention: ≥80 % of all delivered nitrogen. [ABSTRACT FROM AUTHOR]