Both modern and historical data show that lake systems are undergoing profound changes because of human impacts from local to global scales. Research on this topic shows that human pressure on water systems can take various forms and is highly variable in time and space. This article presents the results of Ostracoda fauna research as an indicator of anthropogenic changes covering the time span from 7000 BP to the Mediaeval Period. The palaeoecological information (abundance and habitat preferences of Ostracoda assemblages) obtained in studies of fossil Ostracoda fauna communities amplified by palynological and archaeological data allowed to answer the following questions: (1) to what extent the impact of successive archaeological settlement cultures caused ecological changes in the lake catchment areas without directly affecting the lakes themselves, and when anthropogenic pressure caused transformations in the functioning of lake ecosystems and (2) whether the neolithization, as the first clearly legible stage of anthropopression, had a decisive influence on the functioning of lake ecosystems. Results of Ostracoda fauna studies have been compared with archaeological data available in the literature and multiproxy paleoenvironmental data previously published in a study of lake sediments in the Chełm Hills in South-Eastern Poland. Presented results of study of Ostracoda in lake sediments as a bioindicators of anthropogenic impact suggest that the pressure of prehistoric settlement in older phases (up to the early Middle Ages) was most clearly reflected in the landscape, while the functioning of lake ecosystems was disturbed only by the periodic increase in lake trophic status. A substantial change resulting from the analysis of the subfossil Ostracoda in all the studied lake ecosystems occurred in the phase of settlement related to the Early Middle Ages, which was reflected in the permanently changed species composition of the fauna.