A field experiment was conducted during kharif seasons of 2012 and 2013 at Zonal Agricultural Research Station, Mandya to study the effect of sources of nutrients on productivity, profitability and nutrient uptake of rice (Oryza sativa L.) under different methods of cultivation. The experiment was laid out in a split plot design with three different methods of rice cultivation as main plot i. e. conventional method, system of rice intensification (SRI) and aerobic method and sub-plot treatment as five sources of nutrients including both organic sources and inorganic sources and replicated thrice. Among the different methods of rice cultivation, aerobic method of rice cultivation recorded significantly lower methane emission (3.95 mg/plant/day) and total methane production (24.21 kg/ha) as compared to SRI method (4.42 mg/plant/day and 28.07 kg/ha) and conventional method (6.25 mg/plant/day and 80.68 kg/ha) at 90 days after sowing. Among sources of nutrients, application of RDF (100% neem coated urea) recorded significantly lesser methane emission (4.35 mg/plant/day) and total methane production (37.93 kg/ha) compared to other sources of nutrients but higher methane emission and production resulted by application of 50% N through paddy straw incorporation+50% N through urea+Rec. P & K (5.56 mg/plant/day and 50.45 kg/ha) at 90 DAS. Significantly higher water productivity recorded in SRI method of rice cultivation (54.37 kg/ha-cm) compared to conventional method (46.64 kg/ha) and aerobic method of rice cultivation (29.91 kg/ha-cm). Among sources of nutrients, RDF (100% neem coated urea) recorded significantly higher water productivity (50.40 kg/ha-cm) compared to other sources of nutrients but lower water productivity was recorded by application of 50% N through paddy straw incorporation +50% N through urea+Rec. P & K (36.30 kg/ha-cm).