Recent estimates have confirmed that inland waters emit a considerable amount of CH4 and CO2 to the atmosphere at the regional and global scale. But these estimates are based on extrapolated measured data and lack of data from inland waters in arid and semi-arid regions and carbon sources from wastewater treatment plants (WWTPs) as well insufficient resolution of the spatiotemporal variability of these emissions. Through this study, we analyzed monthly hydrological, meteorological and water quality data from three irrigation and drinking water reservoirs in the lower Jordan River basin and estimated the atmospheric emission rates of CO2. We investigated the effect of WWTPs on surrounding aquatic systems in term of CH4 and CO2 emission by presenting seasonally resolved data for dissolved concentrations of both gases in the effluents and in the receiving streams at nine WWTPs in Germany. We investigated spatiotemporal variability of CH4 and CO2 emission from aquatic ecosystems by using of simple low-cost tools for measuring CO2 flux and bubble release rate from freshwater systems. Our estimates showed that reservoirs in semi-arid regions are oversaturated with CO2 and acted as net sources to the atmosphere. The magnitude of observed fluxes at the three water reservoirs in Jordan is comparable to those from tropical reservoirs (3.3 g CO2 m-2 d-1). The CO2 emission rate from these reservoirs is linked to changes of water surface area, which is the result of water management practices. WWTPs have been shown to discharge a considerable amount of CH4 (30.9±40.7 kg yr-1) and CO2 (0.06±0.05 Gg yr-1) to their surrounding streams, and emission rates of CH4 and CO2 from these streams are significantly enhanced by effluents of WWTPs up to 1.2 and 8.6 times, respectively. Our results showed that both diffusive flux and bubble release rate varied in time and space, and both of emission pathways should be included and variability should be resolved adequately in further sampling and measuring strategies. We conclude that future emission measurements and estimates from inland waters may consider water management practices, carbon sources from WWTPs as well spatial and temporal variability of emission.