Background Climate extremes such as drought and flood have become major constraints to the sustainable rice crop productivity in rainfed environments. Availability of suitable climate-resilient varieties could help farmers to reduce the grain yield losses resulting from the climatic extremities. The present study was undertaken with an aim to develop high-yielding drought and submergence tolerant rice varieties using marker assisted introgression of qDTY 1.1 , qDTY 2.1 , qDTY 3.1 and Sub1. Performance of near isogenic lines (NILs) developed in the background of Swarna was evaluated across 60 multi-locations trials (MLTs). The selected promising lines from MLTs were nominated and evaluated in national trials across 18 locations in India and 6 locations in Nepal. Results Grain yield advantage of the NILs with qDTY 1.1   + qDTY 2.1  +  qDTY 3.1  +  Sub1 and qDTY 2.1  +  qDTY 3.1  +  Sub1 ranged from 76 to 2479 kg ha − 1 and 396 to 2376 kg ha − 1 under non-stress (NS) respectively and 292 to 1118 kg ha − 1 and 284 to 2086 kg ha − 1 under reproductive drought stress (RS), respectively. The NIL, IR96322–34-223-B-1-1-1-1 having qDTY 1.1   + qDTY 2.1  +  qDTY 3.1  +  Sub1 has been released as variety CR dhan 801 in India. IR 96321–1447-651-B-1-1-2 having qDTY 1.1  +  qDTY 3.1  +  Sub 1 and IR 94391–131–358-19-B-1-1-1 having qDTY 3.1  +  Sub1 have been released as varieties Bahuguni dhan-1′ and ‘Bahuguni dhan-2’ respectively in Nepal. Background recovery of 94%, 93% and 98% was observed for IR 96322–34-223-B-1-1-1-1, IR 96321–1447-651-B-1-1-2 and IR 94391–131–358-19-B-1-1-1 respectively on 6 K SNP Infinium chip. Conclusion The drought and submergence tolerant rice varieties with pyramided multiple QTLs can ensure 0.2 to 1.7 t ha − 1 under reproductive stage drought stress and 0.1 to 1.0 t ha − 1 under submergence conditions with no yield penalty under non-stress to farmers irrespective of occurrence of drought and/or flood in the same or different seasons.