The reference condition and historical variability of aquatic ecosystems are key ecological characteristics for understanding the ecological environmental protection and lake ecosystem restoration. Based on chironomid records from 32 lakes in the Jianghan floodplain, this study aims to determine their ecological, chemical reference conditions and the historical variability and its controlling factors. Mesotrophic and macrophyte-related species Paratanytarsus penicillatus-type, Microchironomus tener-type, Cricotopus sylvestris-type, Polypedilum nubifer-type, Dicrotendipes nervosus-type, Procladius etc, were most abundant in the reference samples. Eutrophic-and pollution-tolerate species Chironomus plumosus-type, Microchironomus tabarui-type, Procladius, Propsilocerus akamusi-type, Tanypus etc, were more abundant in the modern samples. Cluster analysis of chironomid composition data from 32 lakes based on eutrophication identified three clusters, 21 out of the 32 lakes experienced significant change. Nutrient input from the catchment and destruction of aquatic vegetation were key factors that explained the significant species change. This study introduces the application of chironomid paleoecology techniques in reconstructing the historical, ecological characters of lake ecosystems, which will provide essential information for the management of wide ranges of wetland.