Flagellates and ciliates were studied over one year, with 52 species identified including 17 flagellates and 35 ciliates. Flagellates were numerically dominant and included cryptomonads, dinoflagellates, and euglenoids. Ciliates included prostomatians, oligotrichs, and gymnostomatians. Species composition and abundance remained consistent spatially but varied seasonally, with flagellates most abundant pre-monsoon and post-monsoon while ciliates followed similar patterns. Cluster analysis identified two flagellate assemblages and three ciliate assemblages dominated by different species. The dam-side protozoan community differed from catchment areas in presence of indicator