The present study was carried out on three different fish farms in Khafr El-Sheikh province. Water samples were collected during three growing seasons: spring, summer and autumn 2018. The seasonal variations of the physicochemical parameters of aquatic samples showed some different magnitudes in these farms. Data on the drainage units of these fish farms are higher than those of the fish culturing ponds apart from those of BOD, Al, Mn and Fe. This could mainly be attributed to the metabolites of the various developing fish stages and/or contaminants in the agricultural drainage. Ammonia and chlorine concentrations exceeded slightly the universal levels, while nitrate and phosphate altitudes were lower than the permissible international standards. It was proved that the protistan organisms (16 genera) of the present study could be divided into four groups depending on the numerical densities; most common, common, frequent and rare protozoan organisms. Certain statistical applications of the present data illustrated that the protozoa were significantly affected by a combination of one and/or more parameters in both culturing and drainage fish units in Kafr El-Sheikh province. Due to certain biotic and abiotic interactions besides statistical evidence in these fish farms, a case of chemostat ecosystem was established.