Abstract Purpose To assess 1) the cumulative greenhouse gas emissions –GHG- and global warming potential (methane – CH₄- and nitrous oxide) from rice fields in the growing and fallow seasons, and 2) the environmental and agronomic drivers of CH₄ emissions, and their relative capacity to explain CH₄ variation. Methods A two-year multisite field experiment covering the agronomic and environmental variability of a rice growing area in NE Iberian Peninsula was conducted with monthly samplings of GHG and monitoring of both environmental and agronomic factors. Information-theoretic framework analysis was used to assess the relative contribution of the environmental and agronomic variables on methane emissions. Results Two thirds of the CH₄ is emitted in the fallow season. Edaphic factors exert more influence during the growing season whereas agronomic factors have a higher impact in the fallow. The implications of these findings on the design of improved mitigation options rice are discussed. Conclusions Soils with higher soil sulphate concentration, bulk density and clay content emit less CH₄ in growing season. In the fallow season, the rates of both straw input and nitrogen fertilization stimulate CH₄ emissions. Graphical abstract