We hypothesize that reservoirs in drier areas have lower CO2 concentration in the water compared to reservoirs in a wetter river basin within a semi-arid tropical region. We also predicted higher bacterial metabolism in dry regions, because drought-induced water deficit increases nutrients concentration and algal biomass. To test this, we compared limnological variables, pCO2 and microbial metabolism in reservoirs from two watersheds with differing precipitation patterns in the Brazilian semi-arid. Reservoirs pCO2 were lower in the driest region, whereas a reversed pattern was observed for nutrients, chlorophyll-a and bacterial metabolism. Consequently, the rainfall decline predicted for the future scenarios should decrease the CO2 saturation, although the microbial metabolism should speed up. Thereby, rainfall decline tends to enhance eutrophication due to increasing nutrients resulting from increased water deficit. Thus, increased primary production declines CO2 saturation, although organic carbon mineralization by microorganisms also increases. Chances are that reservoirs primary production becomes carbon limited once increased CO2 release via decomposition does not result in increased net CO2 accumulation in the water. Increased droughts may negatively impact CO2 accumulation in the atmosphere, but caution is needed when considering this information in regional or global carbon budgets because eutrophication may also increase methane emissions.