Reservoirs around the world contribute to cycling of carbon dioxide (CO2) with the atmosphere, but there is little information on how ecosystem processes determine the absorption or emission of CO2. Reservoirs are the most prevalent freshwater systems in the arid southwest of North America, yet it is unclear whether they sequester or release CO2 and therefore how water impoundment impacts global carbon cycling. We sampled three reservoirs in San Diego, California, weekly for one year. We measured seasonal variation in the abundances of bacteria, phytoplankton, and zooplankton, as well as water chemistry (pH, nutrients, ions, dissolved organic carbon [DOC]), which were used to estimate partial pressure of CO2 (pCO2), and CO2 flux. We found that San Diego reservoirs are most often undersaturated with CO2 with respect to the atmosphere and are estimated to absorb on average 3.22 mmol C m-2 day-1. pCO2 was highest in the winter and lower in the summer, indicating seasonal shifts in the magnitudes of photosynthesis and respiration associated with day length, temperature and water inputs. Abundances of microbes (bacteria) peaked in the winter along with pCO2, while phytoplankton, nutrients, zooplankton and DOC were all unrelated to pCO2. Our data indicate that reservoirs of semi-arid environments may primarily function as carbon sinks, and that carbon flux varies seasonally but is unrelated to nutrient or DOC availability, or the abundances of phytoplankton or zooplankton.