The distribution of benthic invertebrates and their subfossil remains was examined within the basin of De Waay, a dimictic, eutrophic lake in the Netherlands. We focused on Chironomidae, but also report the abundances of 11 invertebrate groups that potentially produce chitinous remains that are preserved in the fossil record, although their remains could only be identified at a coarser taxonomic resolution. Most living invertebrates sampled in different seasons were constrained to the littoral zone, with the exception of a few taxa (Ceratopogonidae, Chaoborus flavicans, and Chironomus) that are adapted to low oxygen conditions in the seasonally anoxic profundal zone. In contrast, assemblages of invertebrate remains in lake surface sediments were similar in the entire lake basin, suggesting that considerable numbers of invertebrate remains are transported and redeposited off-shore in Lake De Waay, due to its steep bathymetry. These results indicate that a single sediment sample obtained from the centre of this lake contains subfossil invertebrate remains originating from the entire lake basin. In Lake De Waay, the majority of taxa found in the living assemblages were identified as remains in lake surface sediments, at least for the Chironomidae that could be identified at a similar taxonomic level in living and subfossil assemblages. Of the total 44 chironomid taxa found in Lake De Waay, 35 taxa occurred in the living assemblages and 34 taxa occurred in the subfossil assemblages. Thirty chironomid taxa occurred both as living and subfossil specimens, and on average these 30 taxa represent 94% of the specimens encountered in a sediment sample. Five rare chironomid taxa present as living larvae were not detected in the subfossil assemblages. Conversely, eight rare and four common chironomid taxa were found in subfossil remains, but not in living assemblages. Our results indicate that subfossil assemblages in surface sediment samples provide spatially integrated and representative samples of the living assemblage. However, a combined approach examining both the living benthic invertebrate fauna and invertebrate remains in lake surface sediments will potentially give a more complete and detailed overview of benthic invertebrates in a lake ecosystem than an approach based exclusively on one of these groups.