We analysed the occurrence of ostracods in a small river, taking into account all the types of water bodies in the floodplain − these included helocrenes, oxbow lakes, and ponds, as well as the main river channel. The objective of the study was to investigate the variation in ostracod communities and identify those factors determining species distribution. The environmental factors considered were the type of water body, responsible for 17% of the variance, the physical and chemical water properties (29%), and the biotic and abiotic factors associated with the substrate type (23%). Among the factors associated with the substrate, sediment sorting, plant coverage and insolation were the most important. The ostracod fauna of the helocrenes differed from that of the other water bodies in the floodplain. In the water bodies of the Krąpiel valley and in the main river channel, 33 ostracod species were recorded, of which 26 were found in the main river channel. Refugia in the floodplain were the main source of the diversity and abundance of ostracods in the main river channel. The mean density in the main river channel was very low, at 330 indiv. m−2, while in the water bodies of the floodplain it was the greatest, reaching up to 5568 indiv. m−2.