Understanding the ecology of bioindicators such as ostracods is essential in order to reconstruct past environmental and climate change from analysis of fossil assemblages preserved in lake sediment cores. Knowledge of the ecology of ancient Lake Ohrid’s ostracod fauna is very limited and open to debate. In advance of the Ohrid ICDP-Drilling project, which has potential to generate high-resolution long-term paleoenvironmental data of global importance in paleoclimate research, we sampled Lake Ohrid and a wide range of habitat types in its surroundings to assess 1) the composition of ostracod assemblages in lakes, springs, streams, and short-lived seasonal water bodies, 2) the geographical distribution of ostracods, and 3) the ecological characteristics of individual ostracod species. In total, 40 species were collected alive, and seven species were preserved as valves and empty carapaces. Of the 40 ostracod species, twelve were endemic to Lake Ohrid. The most common genus in the lake was Candona, represented by 13 living species, followed by Paralimnocythere, represented by five living species. The most frequent species was Cypria obliqua. Species with distinct distributions included Heterocypris incongruens, Candonopsis kingsleii, and Cypria lacustris. The most common species in shallow, flooded areas was H. incongruens, and the most prominent species in ditches was C. kingsleii. C. lacustris was widely distributed in channels, springs, lakes, and rivers. Statistical analyses were performed on a “Lake Ohrid” dataset, comprising the subset of samples from Lake Ohrid alone, and an “entire” dataset comprising all samples collected. The unweighted pair group mean average (UPGMA) clustering was mainly controlled by species-specific depth preferences. Canonical Correspondence Analysis (CCA) with forward selection identified water depth, water temperature, and pH as variables that best explained the ostracod distribution in Lake Ohrid. The lack of significance of conductivity and dissolved oxygen in CCA of Ohrid data highlight the uniformity across the lake of the well-mixed waters. In the entire area, CCA revealed that ostracod distribution was best explained by water depth, salinity, conductivity, pH, and dissolved oxygen. Salinity was probably selected by CCA due to the presence of Eucypris virens and Bradleystrandesia reticulata in short-lived seasonal water bodies. Water depth is an important, although indirect, influence on ostracod species distribution, which is probably associated with other factors such as sediment texture and food supply. Some species appeared to be indicators for multiple environmental variables, such as lake level and water temperature.