Lowland rivers are assumed to be a net source of carbon dioxide (CO2) and methane (CH4). However, little is known about the contribution of marginal permanent and temporary riverine aquatic systems to river carbon metabolism. Elevation, in relation to flooding, hydro‐morphological, and ecological features of such habitats, can affect the gas fluxes across the water–atmosphere interfaces and the periodically air‐exposed riverbeds. This hypothesis was investigated in the lowland sector of the Po River (Northern Italy) from May to September 2008. Five different aquatic habitats were considered: the main river course; a backwater habitat; and three lateral lentic waterbodies—an oxbow and two quarry lakes of different age. The water mass was always CO2 and CH4 supersaturated, and gas fluxes were from the water to the atmosphere. In the highly dynamic river course and backwaters, CO2 emission rates were nearly one order of magnitude greater than in the lentic and hypoxic oxbow and quarry lakes. By contrast, CH4 fluxes peaked in the lentic, deeper, and permanent water bodies. At sediment–atmosphere interfaces, the CO2 emissions increased along an organic matter, a water saturation, and a chlorophyll a gradient, attaining the maximum rates in the periodically air‐exposed riverbed and marginal sandy sediments. These differences in gas fluxes resulted from either the submersion persistence or the alternation of submersion and emersion phases, which were ultimately due to the gap between elevation and river water variations. All this stresses the critical role of marginal aquatic habitats for river C budget.