Improving the productivity of limited land and water resources is necessary to meet the increasing demand for food and feed. A 2-year (2016–18) field study was conducted in a humid climate in the north of Iran to examine the effect of different drainage systems on green water-use efficiency (GWUE), economic water productivity (EWP) and yield and growth indices of winter canola. The treatments consisted of surface drainage (Control) and three conventional subsurface drainage systems. Leaf area index (LAI) and total dry weight were measured randomly during different growth stages. The traits were then used to determine crop growth rate and relative growth rate. Subsurface drainage significantly improved yield and growth indices as well as GWUE and EWP compared with Control, with grater effectiveness under wet season. Yield, GWUE and EWP increase in subsurface drainage systems compared to surface drainage ranged from 460–890 and 825–1090 kg ha−1, 0.13–0.25 and 0.22–0.29 kg m−3 and 0.04–0.08 and 0.07–0.09 US $ m−3 in 2016–2017 and 2017–2018 growing seasons, respectively. Mean LAI in the subsurface drained area was 23–24% and 5–10% more than that in Control in the first and second growing seasons, respectively. The results indicated that an appropriate subsurface drainage system as well as a management strategy is necessary to prevent potential adverse effects of waterlogging in wet seasons and to increase land and water productivity in the study area.