Intra-lake variation of fossil Cladocera (Crustacea) assemblages in 31 surface sediment samples in Lake Pieni-Kauro and River Saavanjoki, eastern Finland, was examined with an objective to identify habitat specificity of Cladocera in relation to local hydrology-related environmental factors. The surface sediment assemblages showed high levels of heterogeneity, mainly as to water depth and lenticlotic gradients in the lake-river complex. This was evident from the principal component analysis which indicated a major trend from shallow to deep samples and a secondary trend from lentic to lotic samples, and from redundancy analysis (RDA), which recognized water depth and river flow as the most important environmental variables in explaining cladoceran variability within the dataset. According to the RDA and generalized linear models, Daphnia spp., Bosmina (Eubosmina), and Alona quadrangularis showed association with deep water localities, whereas Bosmina longirostris and Alona affinis preferred littoral habitats. Acroperus harpae and Chydorus sphaericus s.l. appeared to favor lotic habitats. The results propose that littoral taxa are primarily deposited postmortem or after molting close to their shallow water habitats, while planktonic cladocerans accumulate principally in deepwater locations. Accordingly, it appears that in heterogeneous basins intra-lake surface sediment samples integrate locally living fauna that is driven by local hydrology-related factors, such as water depth, sediment properties, macrophytes, and river flow and coupling biotic interactions.