The objective of the study was to investigate the effect of different species of fish on the qualitative and quantitative structure of microorganisms (ciliates and rotifers) based on an experiment conducted in ex situ conditions. The effect of certain physical and chemical water parameters on the structure of the analysed groups of microorganisms was also analysed. The experiment was conducted in five experimental variants: the control variant (I) and variants involving juvenile perch (II), roach (III), bream (IV) and mixed species (V) (included specimens of roach, perch and bream). Both the qualitative and quantitative structure of microorganisms proved to be substantially impoverished in the experiment dominated by bream. The lowest pressure of fish on microbial communities was observed in the experimental variant dominated by perch.