Research on lake-catchment and biological processes is still innovative. Few reports on this topic exist in the scientific literature. This paper presents species richness, diversity, biomass composition of phytoplankton, and occurrence of cyanobacterial blooms in relation to complex lake-catchment processes in four shallow lakes. The results revealed that phytoplankton species richness increased with increasing lake trophic state, whereas the opposite relationship was observed for phytoplankton biodiversity. In less eutrophic and deeper lakes, the majority of dominant taxa were representatives of mixed, meso to eutrophic small- and medium-sized lakes. In highly eutrophic lakes, the dominant taxa were common representatives of shallow, very rich in nutrients, turbid, mix layers, and eu-hypertrophic environments. Redundancy analysis showed that lake depth, flushing time, and conductivity were the most significant factors for phytoplankton development and composition. The hypertrophic, polimictic, and flow-through Lake Syczyńskie was the most dynamic ecosystem among the lakes. Water mixing and high concentrations of P-PO4 were beneficial for heavy blooms of the cyanobacterium Planktothrix agardhii observed in Lake Syczyńskie despite the high rate of water exchange. Contrary to the findings of some previous studies, P. agardhii seems to be resistant to flushing at very high loads and concentrations of nutrients (mostly of P-PO4 and N-NO3). Phytoplankton assemblages reflected the lakes' habitats, trophic status, and lake-catchment processes and revealed complex factors that influenced the lakes' functioning. The use of phytoplankton as an indicator of lake-catchment processes may help understand ecosystem dynamics, essential for the proper selection of management practices protecting aquatic systems against eutrophication.