The performance of duckweed and algal systems in removing fecal bacteria, organic matter, and nutrients was evaluated in three full‐scale ponds operating in series. Trucks collected septage from holding tanks and discharged it into the system, daily. The inflow rates varied between the warm and the cold season. Duckweed and algae naturally colonized the ponds in two successive periods of 10 and 13 months, respectively. Environmental conditions were determined at various pond depths. Without harvesting, the duckweed system was neutral and anoxic. Alkaline and oversaturation conditions were observed in the algal system. The overall removals of 5‐day biochemical oxygen demand, total suspended solids, total nitrogen removal, and orthophosphate (ortho‐PO43–) ranged from 94 to 97, 62 to 84, 68 to 74, and 0 to 26%, respectively. The E. coli and enterococci reductions varied between 2.2 to 3.0 and 1.1 to 1.4 log units, respectively. The upper values were always associated with the algal system.