Dreissenid management has focused primarily on chemical tools which are efficacious, but not without ecological or economic costs. There is a need for additional control tools that are less expensive, readily available, and will not leave a residue after treatment. Carbon dioxide has these advantages over chemical pesticides and has demonstrated effectiveness for control of a range of aquatic invasive species, including dreissenid mussels. Carbon dioxide was lethal to adult zebra mussels at levels that were safe to juvenile unionid mussels and lower levels cause detachment and gaping. Dreissenid veligers are more sensitive than adults to water quality conditions, including pH. Therefore, we hypothesized that effective PCO2 levels to prevent veliger settlement would be less than levels needed to detach adults; additionally we predicted that effective levels of PCO2 would also prevent colonization of more pH-sensitive native species, especially calcifying organisms, and alter invertebrate and periphyton community composition. In the present study, we simulated a scenario for preventing settlement of zebra mussel veligers in a closed system (water intake system) or a limited open water application. Our test system was continuously supplied with a natural source of veligers, phytoplankton, and invertebrates to colonize the test tanks. We compared veliger settlement and community composition of periphyton and invertebrates between the control and two levels of CO2. The study site is used by the U.S. Fish and Wildlife Service for seasonal propagation of native unionid mussels and culture cages are routinely cleaned to prevent biofouling by zebra mussels. Therefore, we also evaluated survival, growth, and condition of two unionid species across treatments to determine the safety of CO2 at the site. Finally, we considered the potential recapture of CO2 by phytoplankton and macrophytes in the effluent tanks of the system to neutralize carbon input.