Nitrate (NO3−N) export from row crop agricultural systems with subsurface tile drainage continues to be a major water quality concern. Woodchip bioreactors are an effective edge-of-field practice designed to remove NO3−N from tile drainage. The NO3−N removal rate of woodchip bioreactors can be impacted by several factors, including hydraulic residence time(HRT). This study examined the impact of three HRTs, 2 h, 8 h, and 16 h, on NO3−N removal in a set of nine pilot-scale woodchip bioreactors in Central Iowa. NO3−N concentration reduction from the inlet to the outlet was significantly different for all HRTs (p < 0.05). The 16 h HRT removed the most NO3−N by concentration (7.5 mg L−1) and had the highest removal efficiency at 53.8%. The 8 h HRT removed an average of 5.5 mg L−1 NO3−N with a removal efficiency of 32.1%. The 2 h HRT removed an average of 1.3 mg L−1 NO3−N with a removal efficiency of 9.0%. The 2 h HRT had the highest NO3−N mass removal rate (MRR) at 9.0 g m−3 day−1, followed by the 8 h HRT at 8.5 g m−3 day−1, and the 16 h HRT at 7.4 g m−3 day−1, all of which were statistically different (p < 0.05). Significant explanatory variables for removal efficiency were HRT (p < 0.001) and influent NO3−N concentration (p < 0.001), (R2 = 0.80), with HRT accounting for 93% contribution. When paired with results from a companion study, the ideal HRT for the bioreactors was 8 h to achieve maximum NO3−N removal while reducing the impact from greenhouse gas emissions.