A three-year field study was conducted to explore the use of Conservation Agriculture (CA) as a cost-effective alternative to conventional tillage (CT) in rice-wheat (RW) systems. Therefore, to minimize the weed menace while sustaining the system productivity, a three-year field study was undertaken with different CA-based practices layered with flooded (FI) and subsurface drip irrigation (SDI). In rice, weed density (WD) in Sc8 {Zero tillage direct seeded rice with residue (+R) and SDI} recorded 72.9% lowered then Sc1 (CT-Puddled transplanted rice) after three years. However, maximum WD (162 m−2) and dry matter (WDM; 772.8 g m−2) were recorded in ZTDSR without residue (-R) with FI (Sc3) during third year which reduced rice yield by ∼37%. In wheat, the WD and WDM of Phalaris minor, Coronopus didymus, Melilotus indica and other species lowered in CA with SDI system (Sc5-Sc8) than CTRW system (Sc1 and Sc2). Lowest weed index (WI) observed with Sc8 during third year, while diversity indices (H’, R, E) increased by 10, 57 and 10% under SDI system than CTW-R scenario (Sc1). CA-system improved productivity by 7.40–37.11% over CTRW systems in weed free (WF) conditions, regardless of residue and irrigation management. Under weedy check (WC), Sc8 was top yielder with yield of 8.32 Mg ha−1. Moreover, sustainable intensification (Sc7-Sc8) improved productivity by 35.2 and ∼52% than CTRW systems in WF and WC plots, respectively. In conclusion, CA+SDI scenarios may be recommended for RW system owing to their system yield enhancement, resource savings and weed reduction advantages.