Heterogeneous benthic methane (CH4) dynamics from river deltas with important organic matter accumulation have been recently reported in various aquatic and marine environments. The spatial heterogeneity of dissolved CH4 concentrations and associated production and diffusion rates were investigated in the Rhone River Delta of Lake Geneva (Switzerland/France) using sediment cores taken as part of the éLEMO Project. Benthic CH4 dynamics within the complex subaquatic canyon structure of the Rhone Delta were compared (1) between three canyons of different sedimentation regimes, (2) along a longitudinal transect of the ‘active’ canyon most influenced by the Rhone River, and (3) laterally across a canyon. Results indicated higher CH4 diffusion and production rates in the ‘active’ compared to the other canyons, explained by more allochthonous carbon deposition. Within the active canyon, the highest diffusion and production rates were found at intermediate sites further along the canyon. Stronger resuspension of sediments directly in front of the river inflow was likely the cause for the variable emission rates found there. Evidence also suggests more CH4 production occurs on the levees (shoulders) of canyons due to preferred sedimentation in those locations. Our results from the heterogeneous Rhone delta in Lake Geneva further support the concept that high sedimentary CH4 concentrations should be expected in depositional environments with high inputs of allochthonous organic carbon.