Controlled drainage combined with winter crops was investigated for the first time as a mitigation measure for reducing nitrate loss through drainage systems during a three-year period (2012–15) on a loamy soil in Denmark. The impact of controlled drainage on groundwater levels, drain flow, total nitrogen, nitrate, ammonium, nitrous oxide, total phosphorous, and phosphate when applying regulation levels of 50 and 70 cm above drain pipes were determined by using a before-after control-impact (BACI) study design. The regulation level had to be 70 cm to significantly elevate groundwater levels and reduce drain outflow and nitrate loss, which were reduced by 38–52 % (97–127 mm) and 36–48 % (6–8 kg nitrate-N ha^−1) relative to conventional drainage levels, respectively. Controlled drainage did not appear to influence harvest yield or cause pollution swapping as the loss of total phosphorous, phosphate, and nitrous oxide was reduced by 44–45 %, 44–54 %, and 36–38 %, respectively. Stable isotope analysis of δ¹⁵N and δ¹⁸O in nitrate from drain water supported by measurements of nitrate, sulphate, and ammonium concentrations in drain water revealed that denitrification was not enhanced markedly at the impacted plots, except during one event where a pronounced decline in nitrate concentrations and ceased drain flow was observed.