Drainage management is important in intensification of irrigated paddy rice production. This study assessed the effects of drainage intensity on water and nitrogen use efficiency and rice grain yield in a field experiment conducted during three seasons in Rwanda. The experiment comprised 12 plots with four blocks and three treatments: DS 0.6 (0.6 m deep drain), DD1 1.2 (1.2 m deep drain, control structure open four times per week), and DD2 1.2 (1.2 m deep drain, control structure open two times per week). Outflow was calculated from water balance. Nitrogen (N) content in drainage water was determined weekly. Crop yield and N uptake were determined in grain and straw. In all seasons, grain yield was 61-131% higher, crop N uptake was 24-90% higher, harvest index (HI) was 24-65% higher and water use efficiency (WUE) was 50-150% higher in treatments DD1 1.2 and DD2 1.2 than in DS 0.6. There was a decrease in soil carbon/nitrogen ratio at the end of Seasons 2 and 3. Recirculating straw to fields is thus necessary to replenish SOC for long-term soil fertility. A practical implication of the study is that managed deep drainage systems could enhance water use efficiency and rice grain yield in poorly drained paddy fields.