The aim of this study was to examine the diel dynamics of the qualitative and quantitative structures of psammonic ciliates and rotifers in a shallow eutrophic lake. Furthermore, the effects of specific physical and chemical factors of water on the occurrence of microorganisms were analyzed. There were clear differences in the qualitative and quantitative structure of organisms between the examined micro-habitats in a diurnal cycle. The highest density of ciliates, irrespective of the time of day, was recorded in the higroarenal zone, while the highest density of rotifers was found in both the higro- and hydroarenal zones. The lowest diversity of ciliates was recorded in the hydroarenal zone. RDA analysis showed a clear contrast between the eupsammonic, higropsammonic, and hydropsammonic zones, regardless of the time of day. A direct impact on the occurrence of protozoa and small Metazoa was played by the content of total phosphorus (P_tot) and TOC in the water. In addition, the ciliates were significantly affected by P-PO₄ and N-NO₃, and also the pH affected the group of rotifers.