Subfossil Cladocera analysis allows discussion of the influence of human activity on the lake environments from Neolithic times up to the present. Three lakes were chosen for the analysis: two in northern Poland and the third on Cres Island, Adriatic Sea (Croatia). During the Holocene the species composition and the specimen abundance often changed, resulting mainly from climate changes, and also from human activity. This phenomenon is recognized on the diagrams of absolute abundance and percentage ratio of specimens of the pelagic species to the littoral ones. The data from Cladocera analysis were compared with the abundance of some plants reflecting human activity. A large degree of correlation was noted between the increased presence of these plants and the occurrence of the Cladocera species preferring more trophic water. Some phases of increased lake eutrophication were distinguished on the basis of Cladocera species preferring nutrient rich water. According to the comparative palynological and archaeological studies, these phases are correlated with the periods of settler groups’ activity beginning in Neolithic times. The most distinct changes in the species composition of Cladocera have been noted in the lake sediment from the Medieval Period. They were brought on by the agricultural revolution, which has lasted uninterruptedly up to now. It was observed that the intensity of the expressed abundance of index species in sediments is dependent on the size (area and depth) of the lake. The smaller the lake is, the greater is the change in species composition of zooplankton. The smaller water bodies react faster to an excessive supply of eutrophic compounds, and therefore the change is more clearly evident in the sediment record. Considerable secondary influence of these changes on the species composition of plankton was noted in the large lakes: Lednickie Lake (Poland) and Vrana Lake (Adriatic).