Rivers are important contributors to global greenhouse gas (GHG) exchange with the atmosphere. However, much less is known about biogeochemical dynamics in rivers when they dry, particularly in isolated pools created by drying. Our objective was to examine the effects of water temperature and allochthonous organic matter (OM) quantity on carbon dioxide (CO2) and methane (CH4) fluxes in isolated pools. We used an automated analyzer to measure CO2 and CH4 from 36 mesocosms filled with sediments and water from a non-perennial river, with temperature (20, 25, 30 °C) and Alnus glutinosa leaf litter (2g, 5g, 10 g) manipulations in triplicate. We found positive individual effects of water temperature and OM quantity on CO2 fluxes, and a synergistic effect of water temperature and OM on CH4 fluxes during the late stages of the incubation. Given the increase in water temperature and OM inputs in rivers associated with climate change, our results indicate an associated increase in CO2, and a disproportionate increase in CH4 fluxes to the atmosphere, potentially contributing towards a positive climate feedback loop.