Man-made 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. It is essential to determine if reservoirs sequester or release CO₂ to understand how water impoundments impact global carbon cycling. We sampled three reservoirs throughout San Diego, California, all of which receive most of their water from Northern California and the Colorado River, weekly for one year. We measured seasonal variation in the abundances of bacteria, pelagic fungi, phytoplankton, and zooplankton, as well as abiotic factors such as water chemistry (pH, nutrients, conductivity, ions, dissolved organic carbon [DOC] and partial pressure of CO₂ [pCO₂]). We found that San Diego reservoirs are most often undersaturated with CO₂ with respect to the atmosphere and vary seasonally in both different trophic level abundances and pCO₂. pCO₂ was highest in the winter and lower in the summer, indicating seasonal shifts in the magnitudes of photosynthesis and respiration. Microbes (bacteria and fungi) showed peak abundances in the winter, while phytoplankton, nutrients, and DOC were all relatively uncorrelated with pCO₂. Our data indicate that San Diego reservoirs are consistently net photosynthetic and therefore function mainly as sinks of carbon from the atmosphere. pCO₂ was mainly related to seasonal variation in system respiration but not to the abundances of pelagic producers or consumers