Rarity as a multidimensional concept has not been discussed for the ostracods along with the effects of physicochemical factors and sedimentation rates of waters on their distribution. We randomly sampled 91 aquatic sites including eight habitat types in the Çanakkale Province to study ostracod species rarity, commonness, and ecological preferences, and to test the relationships between the rarity index (average of geographic range, habitat specificity, and population size indices) and environmental factors. A total of 44 ostracod taxa (25 living) were reported from 75 sites. Among the species, Candonocypris caledonica was recorded for the first time in Türkiye. Sixty percent of 25 living species exhibited cosmopolitan characteristics, making significant contributions to the diversity of ostracods. The well-known cosmopolitan species, Heterocypris salina (rr = 0.268), Cypridopsis vidua (rr = 0.289), Limnocythere inopinata (rr = 0.330), Ilyocypris bradyi (rr = 0.370), and Psychrodromus olivaceus (rr = 0.390), were identified as common species based on the rarity index (rr) values. Of the environmental variables, only sediment grain sizes (×2000, ×500, and ×63 μm) were found to be effective on the distribution of ostracod species. The Shannon index exhibited a positively significant association with ×2000, while the population size index displayed a linear relationship with ×63 μm grain size, indicating a small population size and rarity. Associations among index values, sediment grain size, and water quality variables showed that comprehensive studies on ostracods, analyzing both water and sediment, can provide a clearer and more precise information for evaluating the rarity and ecological preferences of species.