•CH4 emission was increased by 26% in rice-fish than rice alone.•N2O emission was decreased by 9% in rice-fish with common carp than rice alone.•The GWP and CEE increased by 29.5% in rice-fish with common carp than rice alone.•Rice+common carp in rainfed shallow lowland is economic, higher C credit compliance.•Indian major carps (mrigal rohu and catla) emit less GHGs than common carp. Four fish species namely, Cirrhinus mrigala H. (mrigal), Labeo rohita H. (rohu), Cyprinus carpio L. (common carp) and Catla catla H. (catla) were introduced along with rice (Oryza sativa L.) cv. Varshadhan, in a rainfed shallow (0–25cm water depth) Inceptisol to evaluate the effect of fish species on methane (CH4) and nitrous oxide (N2O) emission in a rice-fish farming system. On seasonal basis, the emission of CH4 was significantly higher by 26% under rice-fish co-culture compared to rice alone. The maximum emission of CH4 (36% higher) was found under rice+common carp farming. On contrary, the emission of N2O was significantly lower by 9% under rice-fish compared to rice alone. Although the global warming potential (GWP) was highest (29.5% more) in rice+common carp, the CH4 and N2O emission from this treatment per unit of total yield (rice+fish) were at par and significantly lower, respectively, compared to rice alone. Further, it provided significantly higher yield (rice+fish) and economic benefit over rice and other rice+fish species combinations. The integration of common carp with rice in rainfed shallow lowland ecology is thus, one of the viable options for livelihood of the small and marginal farmers besides, higher carbon (C) credit compliance. However, Indian major carps, mrigal rohu and catla in order, are potentially less harmful in terms of GHGs emission in shallow rice fields besides, higher profitability and carbon credit compliance compared to rice farming alone.