Methane (CH4) emission and water productivity were estimated in an experiment conducted during wet (rainy) season of 2010 at the research farm of Indian Agricultural Research Institute, New Delhi, India. Treatments comprising three methods of crop establishment viz., conventional transplanting (CT), system of rice intensification (SRI) and double transplanting (DT) were laid out in randomized block design with four replications. Scented rice (Oryza sativa L) variety ‘Pusa Basmati 1401’ was transplanted in puddle field. In CT and SRI 21 and 12-day-old seedlings, respectively, were transplanted while in DT overall 45-day-old seedlings were transplanted. In CT and DT flooded conditions while in SRI saturated conditions were maintained. Results indicated that among the methods of crop establishment, CT had maximum cumulative CH4 emission (32.33 kg ha−1) followed by DT (29.30 kg ha−1) and SRI (19.93 kg ha−1). Temporal CH4 flux fluctuated between 79.7 and 482.0 mg m−2 day−1 under CT; 46.0 and 315.0 mg m−2 day−1 in SRI and 86.7 and 467.3 mg m−2 day−1 in DT. Considerable temporal variations in the individual CH4 fluxes were observed. Flux of CH4 was generally higher in early stage of crop and peaked about 21 days after transplanting coinciding with tillering stage of crop. CH4 flux declined gradually from 75 days after transplanting and stabilized at the harvest stage of rice in all the three methods of transplanting. Global warming potential was highest in CT (807.4 kg CO2 ha−1) and lowest in SRI (498.25 kg CO2 ha−1). However, a reverse trend was observed with carbon efficiency ratio. The water savings to the extent of six irrigations was recorded in SRI over CT. A saving of 27.4 % irrigation water and 18.5 % total water was recorded in SRI over CT while the corresponding values of DT over CT were 14.5 and 9.8 %. Water productivity of SRI (3.56 kg/ha mm) was significantly higher as compared to DT (2.87 kg/ha mm) and CT (2.61 kg/ha mm).