Daytime water quality was determined monthly over two years in an instream series of four urban reservoirs with recurring blooms of Prymnesium parvum—a cool-season toxigenic species. Temperature, pH, and laboratory-measured total alkalinity were used to estimate pCO₂. System-wide, pCO₂ was negatively associated with dissolved oxygen. Chlorophyll-a, phycocyanin (cyanobacterial pigment), and P. parvum were negatively associated with pCO₂ and positively with dissolved oxygen. Three reservoirs were productive and, during daytime, pCO₂-undersaturated year-round or near-year-round, while a fourth (third in the series) was unproductive and mostly pCO₂-oversaturated. Seasonal phycocyanin and chlorophyll-a patterns indicated that cyanobacterial and eukaryotic (P. parvum included) phytoplankton growth drives daytime CO₂ depletion in the productive reservoirs during the warm and cool seasons, respectively. The system’s moderate alkalinity (HCO₃⁻) may serve as an alternative carbon source for photosynthesis; however, the persistent depletion of CO₂ and the energetic cost of using HCO₃⁻ are consistent with a scenario where phytoplankton growth is CO₂-limited. Daytime pCO₂ undersaturation across seasons has been rarely reported, but this study indicated it occurs more often than recognized. The non-monotonic spatial patterns in productivity and carbonate system conditions across the study reservoirs indicate that localized influences from a heterogeneous urban landscape may help shape individual lake metabolism.