Floodplain lakes are rarely analysed for fossil chironomids and usually not incorporated in modern chironomid-climate calibration datasets because of the potential complex hydrological processes that could result from flooding of the lakes. In order to investigate this potential influence of river inundations on fossil chironomid assemblages, 13 regularly inundated lakes and 20 lakes isolated from riverine influence were sampled and their surface sediments analysed for subfossil chironomid assemblages. The physical and chemical settings of all lakes were similar, although the variation in the environmental variables was higher in the lakes isolated from riverine influence. Chironomid concentration and taxon richness show significant differences between the two classes of lakes, and the variation in these variables is best explained by loss-on-ignition of the sediments (LOI). Relative chironomid abundances show some differences between the two groups of lakes, with several chironomid taxa occurring preferentially in one of the two lake-types. The variability in chironomid assemblages is also best explained by LOI. Application of a chironomid-temperature inference model shows that both types of lakes reconstruct July air temperatures that are equal to, or slightly underestimating, the measured temperature of the region. We conclude that, although there are some differences between the chironomid assemblages of floodplain lakes and of isolated lakes, these differences do not have a major effect on chironomid-based temperature reconstruction.