The sedimentary record from lakes can be used as an archive of past environmental changes and for events related to anthropogenic activities in the catchment area. In this paper, we review the more recent studies on zoobenthos responses to changes in lake productivity and to altered sublittoral and hypolimnetic oxygen conditions, as reflected from subfossil midge (Diptera: Chironomidae) assemblages and palaeostratigraphies. We discuss how the importance of different environmental variables is scale dependent in both time and space and we summarize some of the classical and general patterns in chironomid palaeolimnology. The recent advances in quantitative reconstructions using chironomid transfer functions and numerical analyses are presented and compared. A consensus ranking of species trophic optima and respiratory adaptations from published data sets showed good agreement. Factors such as lake depth, stratification patterns, water level change, sediment conditions, submerged vegetation and ecological thresholds are all important for interpretation of palaeolimnological trajectories. We use previously published and new data to document how these factors determine, change or preserve the "lake identity" over time. We conclude that subfossil chironomids have proven to be very effective indicators for lake trophic development (productivity) and hypolimnetic oxygen conditions. Challenges in interpreting the subfossil chironomid record include the interaction between a range of scale-dependent variables and processes.