The influence of CO2 addition and hydraulic retention time (5 and 7 days) on removal of Pseudomonas aeruginosa, Clostridium perfringens, Staphylococcus sp., Enterococcus sp., and Escherichia coli was evaluated in a system with three parallel 21 L high rate algal ponds. Both the addition of CO2 and an increase in HRT had no significant influence on bacterial removal, but bacterial removal was higher than found in previous studies. The removal was 3.4–3.8, 2.5–3.7, 2.6–3.1, 2.2–2.6 and 1.3–1.7 units log for P. aeruginosa, E. coli, Enterococcus sp., C. perfringens, and for Staphylococcus sp., respectively. Although CO2 addition did not increase disinfection, it did significantly increase biomass productivity (by ≈60%) and settleability (by ≈350%). Additionally, even at the lower 5-day hydraulic retention time, CO2 addition improves removal of chemical oxygen demand (COD), total organic carbon (TOC), total organic nitrogen and phosphorus by 97, 91, 12 and 50%, respectively.