To describe the indicator potential of non-marine ostracods for lotic (streams) and lentic (lakes) habitats, 42 taxa (27 recent, 15 subfossil) were evaluated from 62 sampling sites in West-site of Turkey during May of 2018. Nannocandona faba is a new report for Turkey. A higher Shannon diversity value was reported for lakes (H′ = 2.16) than streams (H′ = 1.62) when they had equal number of species (17 spp.). SIMPER analysis showed 53.01% contribution of Psychrodromus olivaceus, Candona neglecta, Heterocypris incongruens and Stenocypria fischeri with a 96.72% difference between lakes and streams. Both TWINSPAN and Indicator Species Analysis revealed that P. olivaceus (p < 0.01) and S. ficheri (p < 0.05) were found to be candidate indicators for the lotic and lentic habitats, respectively. The first two axes of CCA explained 66.90% of the relationship between species and environmental variables when elevation, dissolved oxygen concentration and water temperature showed influential effects (p < 0.05) on the ordination of species. Species with reduced swimming setae (17 spp.) were ordinated relatively closer to the center of CCA. Results showed that ecological tolerances of species seemed to be more deterministic than morphological characters (e.g., swimming setae) on their habitat preferences. A broad knowledge of the morphological and ecological preferences of the species is needed to distinguish whether habitat is chosen by species due to its ecological needs or morphological characteristics. Studies providing information about the current ecological preferences of the species give the opportunity to understand the habitat of these species.