Hydrological intermittency affects sediment biogeochemistry, organic carbon (OC) metabolism and carbon dioxide (CO2) emission but the study of the effects of drying is generally confined to natural ecosystems. Agricultural canals are artificial, widespread elements in irrigated floodplains, and regularly subjected to water level fluctuations. The aim of this study was to quantify the CO2 emissions along water saturation gradients in artificial canals to understand the environmental factors regulating these fluxes. CO2 measurements were performed in five replicated canals within the Po River basin (Northern Italy). In each canal we analysed three sites: (i) a spot with exposed, dry sediments; (ii) a spot with inundated, saturated sediments and (iii) a spot with an intermediate level of saturation. Besides dark CO2 flux measurements, net potential nitrification and denitrification rates were measured as proxies of sediment redox potential and due to their CO2 sink and source role, respectively. We hypothesized a site-specific regulation of CO2 emission, depending on the interplay among water saturation, sediment oxidation and organic matter content. Our results suggest that desiccation stimulates mineralization processes and CO2 fluxes, that were mainly dependant on water and organic matter content and correlated with microbial N transformations. CO2 emissions tended to increase along the considered water saturation gradients, almost tripling rates from inundated, saturated (158.2 ± 24.1 mmol CO2 m−2 days−1) to dry, exposed sediments (416.5 ± 78.9 mmol CO2 m−2 days−1). Results also suggest that net potential nitrification and denitrification allow tracing the effects of drying on N microbial communities involved in CO2 fluxes. Net potential nitrification rates produce little effects on CO2 fluxes, but is a good proxy of oxygen (O2) availability, whereas potential denitrification may be responsible for variable fractions (up to 100%) of CO2 production, in wetter sediments.