We have 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. The data were collected between 2006 and 2013 and show that the reservoirs, which differ in size and age, were net sources of CO2. The estimated surface fluxes were comparable in magnitude to those reported for hydroelectric reservoirs in the tropical and sub-tropical zones. Highest emission rates were observed for a newly established reservoir, which was initially filled during the sampling period. In the two older reservoirs, CO2 partial pressures and fluxes were significantly decreasing during the observation period, which could be related to simultaneously occurring temporal trends in water residence time and chemical composition of the water. The results indicate a strong influence of water and reservoir management (e.g. water consumption) on CO2 emission rates, which is affected by the increasing anthropogenic pressure on the limited water resources in the study area. The low wind speed and relatively high pH favored chemical enhancement of the CO2 gas exchange at the reservoir surfaces, which caused on average a four-fold enhancement of the fluxes. A sensitivity analysis indicates that the uncertainty of the estimated fluxes is, besides pH, mainly affected by the poorly resolved wind speed and resulting uncertainty of the chemical enhancement factor.