The results of an investigation into the relationship between surface sediment subfossil chironomid distribution and water quality are presented. Data from 30 lakes in the middle and lower reaches of the Yangtze River indicate that the nutrient gradient was the major factor affecting the distribution of chironomids across these sites. Canonical correspondence analysis (CCA) revealed that of 12 summer water environmental variables, total Phosphorus was most important, accounting for 20.1% of the variance in the chironomid data. This was significant enough to allow the development of quantitative inference models. A TP inference model was developed using weighted averaging (WA), partial least squares (PLS) and weighted averaging partial least squares (WA-PLS). An optimal two-component WA-PLS model provided a high jack-knifed coefficient of prediction for conductivity r 2 jack = 0.76, with a low root mean squared error of prediction (RMSEPjack = 0.13). Using this model it is possible to produce long-term quantitative records of past water quality for lacustrine sites across the middle and lower reaches of the Yangtze River, which has important implications for future lake management and ecological restoration.