1. The specific effects of three types of anthropogenic forcing (nutrient concentrations, climate change and fisheries management practices) on the benthic invertebrate community over the last 150 years in a re-oligotrophicated large, deep subalpine lake were investigated using chironomid remains. The structural changes in the chironomid assemblages in different habitats were assessed based on subfossil remains retrieved from sediment cores sampled along a depth gradient (30, 56 and 65 m) and analysed at a high temporal resolution (2-5 years). 2. Until the 1940s, the chironomid assemblages were strongly depth specific and were characterised by oxyphilous taxa at all studied depths. Subsequently, the assemblages drifted towards domination by common hypoxia-tolerant taxa. The scores of the first axis of principal component analyses for each studied depth were used as a proxy for community structure, and the influence of anthropogenic forcings on axis scores was assessed using general additive models. The temporal variability of the contribution of each covariate to our model estimates allowed their specific effects to be clarified. 3. The sensitivity of the chironomid assemblages to the considered forcings was depth dependent. Profundal chironomid assemblages (65 m) responded mainly to nutrient enrichment, whereas assemblages at shallower depths (56 and 30 m) were mainly affected by top-down effects of the fish community on the pelagic food web, triggering increasing losses of organic matter from the pelagic to the benthic zone. Since the late 1980s, increased air temperatures have probably been responsible for changes in assemblages at all sampled depths, potentially through their effect on the strength and duration of thermal stratification, possibly coupled with changes in mixing efficiency during winter. 4. Our results highlight linkages between the pelagic and benthic food webs and identify possible temporal substitutions among anthropogenic forcings that successively drive the chironomid assemblages. These findings provide additional evidence of the multiple environmental controls structuring chironomid assemblages and highlight the associated difficulties in predicting chironomid assemblage trajectories following mitigation efforts.