Agricultural activities emit substantial amounts of methane (CH4) and nitrous oxides (N2O), the two important greenhouse gases (GHG) with high global warming potentials (GWP). So far, many studies have already been carried out at national and state level, but lack micro‐level (district or block‐level) inventory in India. The present study sheds light on the flux of CH4 and N2O (from all possible sources) from agricultural soil of various blocks in the Murshidabad district, based on the inventory prepared, using the IPCC methodology, with adjusted emission factors and coefficients appropriate for the local level. The economy of the Murshidabad district almost completely rests on agriculture as more than 80 per cent of the population is directly or indirectly dependent on it for their livelihood. Paddy is the dominating crop, cultivated on more than 60 per cent of the gross cropped area. The present work is based on the review of various literature and reports collected from respective state government offices and websites. Results show that CH4 and N2O emission from the agricultural fields are 126.405 Gg and 0.652 Gg respectively for the year 2011−12 with a large scale spatial variation (block‐level) within the district.