Biological invasions have attracted particular attention since they often result in serious consequences for natural ecosystems. One planktonic invasive species is Cylindrospermopsis raciborskii, a cyanobacterium originally reported to occur exclusively in the tropics. Over the last few decades its range has extended to temperate regions and it occupies shallow highly eutrophic lakes previously dominated by other cyanobacteria. The purpose of this study was to examine the ecology of C. raciborskii during Planktothrix agardhii blooms in two shallow lakes in western Poland and to determine whether these species have different environmental preferences. Multiple linear regression showed that the biomass of P. agardhii was significantly negatively related to Secchi depth in Lake Bnińskie. In Lake Bytyńskie, P. agardhii was significantly positively related to concentrations of , chlorophyll a and total phosphorus and negatively related to Secchi depth, , and total nitrogen. Cylindrospermopsis raciborskii was significantly positively related only to concentrations of . There was a negative correlation between the biomass of P. agardhii and C. raciborskii perhaps showing different responses to environmental variables. Moreover, the biomass of P. agardhii was negatively correlated with Shannon–Wiener diversity of the phytoplankton assemblages. Our results support the concept that these cyanobacterial species have different environmental preferences and their niches differ from each other. These results suggest that light is an important driver of phytoplankton community structure resulting in shifts from a community dominated by P. agardhii in very turbid waters to more diverse communities perhaps including the invasive C. raciborskii in clearer waters.