Chitinous aquatic invertebrate remains are abundant in late Quaternary lake sediment sequences. However, for standard analysis of invertebrate indicator groups usually only the remains of one particular invertebrate group (e.g. water fleas, midges) are systematically isolated from the sediments and analysed numerically. In a calibration study focusing on surface sediment samples from 36 small Swiss lakes, we show that the abundances of other chitinous aquatic invertebrate remains in samples prepared for chironomid analysis provide important information on in-lake oxygen conditions when assessed relative to and together with the overall number of chironomid remains. Our results show that particularly high abundances of chironomid and chaoborid remains are indicative for lakes with high and low deepwater oxygen concentrations, respectively, but that also the remains of other invertebrate groups such as Ceriodaphnia ephippia and Plumatella statoblasts tend to be more abundant in warm, stably stratified and anoxic lakes. Direct gradient analyses of the isolated invertebrate assemblages indicate that deepwater oxygen concentration during late summer is the strongest predictor for assemblage changes in our dataset, followed by variables representing temperature conditions (summer surface water temperature, altitude), summer stratification stability (temperature difference between surface and deepwater layers), water depth and the relative volume of the late summer hypoxic water layer. We show, based on invertebrate assemblages in a Lateglacial sediment sequence from Rotsee, Switzerland, that our new calibration data can provide information on past changes in deepwater oxygen availability from late Quaternary lake sediment sequences, when fossil invertebrate assemblages are added as passive samples to ordinations of the surface sediment calibration data. This provides a new approach for developing assessments of past changes in deepwater oxygen concentrations from late Quaternary sediment samples prepared for chironomid analysis. Such assessments can provide important supplementary information for e.g. interpreting palaeotemperature reconstructions based on chironomid remains.