The recent environmental history of Bosten Lake in Xinjiang, in the arid region of continental NW China, was studied using short core sediment samples extracted from the river mouth and the deep centre of the lake. Based on chironomid stratigraphy and sediment properties, it was possible to distinguish two stages during the past century. The concentration of midge head capsules sharply decreased and the entire chironomid community was overwhelmed around the 1950s due to the rapid accumulation of sediment and the sudden increased proportion of fine grains caused by enhanced human activities (mainly population increase and the subsequent reclamation of alkaline land and agriculture intensification). Chironomus plumosus-type and Microchironomus dominated the chironomid fauna starting in the 1950s. Human activities in the catchment together with climate change exerted significant influence on the chironomid fauna, causing the near disappearance of Procladius and an increase in fine sediment. Environmental changes in the Bosten Lake catchment affected the chironomid fauna in the profundal zone much earlier than in the river mouth zone. We present a case study in order to gain a further insight into the ecological effects of climate change and anthropogenic activities on the chironomid fauna in the arid continental region of NW China. This will assist the definition of 'pre-disturbance' conditions of the lakes in this region and provide baseline information for establishing targets for the management and restoration of the lakes in this vast region.