Chironomidae and Cladocera are useful palaeoindicators to describe long-term dynamics in biodiversity of freshwater aquatic communities. However, palaeoecological studies relying on these aquatic invertebrates have generally focused on post-glacial lakes, with relatively few applications to floodplain water bodies such as palaeo-oxbow lakes. In this study, zone-level (stratigraphic) trends in Chironomidae and Cladocera assemblage composition were analysed from a small palaeo-oxbow lake in a Central European river valley of Poland. Summer air temperature and hydrological conditions were found to be the main drivers of Cladocera and Chironomidae populations, causing a cascade effect in assemblage composition. At the local habitat scale, there were autecological differences in both taxonomic groups reflecting different responses to abiotic and biotic factors. Specifically, Cladocera responded distinctly to plant vegetation and fish predation during the Late Glacial lake phase, whereas Chironomidae were more sensitive to paludification processes and disappeared in the Northgrippian dry phase of the mire. Both groups indicated fluvial activity of the River Grabia, although the response was different. Also, species richness was higher in the more taxonomically diverse Chironomidae compared to Cladocera. As both groups responded to the same factors in a different way, it is recommended that they should be used in parallel in palaeoecological research studies.