There is no doubt that the diversity and stability of freshwater ecosystems have suffered dramatic changes as a result of intensified human activities. However, the relationship between community diversity and stability is still debated. In this study, we used biological and geochemical records from the recent sediments of two lakes to test the hypothesis that different aspects of the diversity of the chironomid community have different relationships with community stability. Yangzong Lake (YZ) and Chenghai Lake (CH) are large and deep alpine lakes in SW China. We conducted a multi-proxy study of the sedimentary records spanning the last 200 years from the two lakes. Our focus was on subfossil chironomid remains, but analyses of chemical elements, total organic carbon (TOC) and total nitrogen (TN) were also conducted. The principal results are as follows: 1) Both nutrient and chironomid assemblages underwent a critical transition in 1990 at YZ and in 1998 at CH. 2) The response of species richness varied between the two lakes, but the trends of their respective β diversity indices are consistent, despite the fact that the contributors to β diversity are different. 3) The stability of the chironomid communities has decreased in both lakes since the mid-20th century. 4) The relationship between diversity and stability varies in relation to the type of diversity. Overall, our results emphasize the importance of considering the complex nature of diversity and stability when studying community assemblages.