A number of studies evidenced the impact of human activities on aquatic environments worldwide. The availability of nutrients in lakes is strongly influenced by watershed land use patterns depending on the share of forestry, agriculture and urbanization level. Nearly all the previous studies, which examined the relationships between the phytoplankton community and the land use pattern on the watershed of lakes or reservoirs were performed on a taxonomic basis. In this study, 78 lakes were sampled to analyse how the different land use types affect their phytoplankton functional group compositions. Our results concluded that land use is a complex driver, and it cannot provide an unequivocally straightforward forecast, which could result in the selection of a specific functional group or taxa. Thus, land use alone is a weak predictor, but the shared effects may structure the phytoplankton assemblage composition.