Abstract Application of livestock manure has become a principal nutrient source in groundwater and surface water. The goal of this research was to investigate the effect of controlled drainage (CD) on nitrogen (N) fate and transport for a subsurface drained grass field receiving liquid swine lagoon effluent (SLE). A four-year field experiment was conducted on a naturally poorly drained pasture in eastern North Carolina. The 1.25 ha experimental field was artificially drained by subsurface drains installed at 1.0 m depth and 12.5 m spacing. Two treatments, replicated twice were implemented: conventional drainage (FD) and CD. The CD management protocol was more intensive compared to previous studies. The drain outlets of CD plot were set at 36 cm below soil surface all year round except several days before irrigation application when water table depth was shallower than 65 cm below surface. Controlled drainage significantly reduced drainage flow and TN loading via subsurface drain lines by an average of 397 mm yr−1 (93%) and 34.5 kg N ha−1 yr−1 (94%), respectively. DRAINMOD hydrologic simulations indicated that 96% of the reduction in predicted drain flow was attributed to increased lateral seepage. The nitrogen that did not drain from the field in response to CD was lost via enhanced denitrification (67%) and lateral seepage to adjacent fields (33%). This study clearly demonstrated how CD management affects the N fate and transport through seepage and denitrification process.