The composition of the protozoan assemblage at a sewage treatment facility may be a good indicator of the efficiency with which the incoming waste is being processed. The structural and functional composition of protozoan assemblages at three sewage treatment facilities, each of which employed a different method, was compared to explore this idea. There were large differences in the number and kinds of protozoan taxa among the three facilities. Despite radical differences in the structure of the three protozoan assemblages, all appeared to perform a similar function and were dominated by bactivorous species. Furthermore, no indication of gross differences in efficiency occurred among the three treatment facilities, despite differences in species richness and composition. The function of the protozoan assemblage appears to be determined by the available resource base, which was similar at all three facilties; differences in the structure of the assemblage may reflect qualitative differences in the manner with which resources (i.e., sewage) are processed at different facilities.