Abstract: Protozoa populations and the types of microbiota were determined at various depths (0.1, 0.35 and 0.63 m) in water lettuce, duckweed and algal ponds receiving medium strength sewage. The role of protozoa on the removal of faecal bacteria was also determined. In the water lettuce and duckweed ponds, protozoa were concentrated in the sediments while the algal ponds protozoa were mostly found in the sediments as well as on the surface. Bodo and Vahlkampfia protozoa were both common in all the 3 pond systems. The protozoan Petalomonas and Chironomus insect larvae were found only in the water lettuce and duckweed ponds. Vorticella and other unidentified ciliates were however unique to the algal ponds. The algal ponds had the highest number of species diversity and the highest number of protozoans, followed by water lettuce and duckweed. Other algae such as Chlorella, Chlorococum, Phacus, Ulothrix and some diatoms were also found but in small quantities. The presence of protozoa was found to have a significant effect in the removal of E. coli and Salmonella (p<0.05) in water lettuce pond system. In the duckweed and algal pond systems however, there was no difference between faecal bacteria removal with respect to protozoa. Results from this study has shown that the protozoa could play a major role in the removal of E. coli and Salmonella in water lettuce treatment ponds.