One of the features of Gonyostomum semen, a bloom-forming and expansive flagellate, is uneven distribution in the vertical water column often observed in humic lakes. In this paper, we analysed vertical distribution of the algae in four small (0.9-2.5 ha) and humic (DOC: 7.4-16.5 mg dm(-3)) lakes with similar morphometric features with the aim to test the hypothesis that vertical distribution of G. semen may be shaped by zooplankton structure and abundance. In addition, we wanted to check whether high biomass of this flagellate has any influence on the chemical composition as well as on planktonic bacteria abundance of the water column. The results of the study showed that vertical distribution of the algae during the day varied among all studied lakes. Our most important finding was that (a) the abundance and structure of zooplankton community (especially in case of large bodied daphnids Daphnia pulicaria, D. longispina and copepod Eudiaptomus graciloides) may shape G. semen vertical distribution in studied lakes; (b) high G. semen biomass may decrease the content of ammonium ions in the water column by intense uptake, but has low effect on other water chemical parameters. The results of the study contribute to the understanding of the factors influencing this expansive algae behaviour as well as it shows interesting aspects of G. semen influence on some components of the lake ecosystem.