Although few reports have described long-term continuous anoxia in aquatic systems, Lake Ikeda in Japan experienced such conditions in the hypolimnion from 1990 to 2010. The present study aimed to assess temporal fluctuations in the lake's thermal stability from 1978 to 2011 to understand the influence of regional climate change on hypolimnetic anoxia in this lake. Because complete vertical mixing, which supplies dissolved oxygen (DO) to the hypolimnion, potentially occurs on February, we calculated the Schmidt stability index (S) in February and compared it with hypolimnetic DO dynamics. Vertical water temperature profiles were calculated using a one-dimensional model, and calculated temperatures and meteorological data were used to analyse annual fluctuations in water temperatures, thermocline depth, meteorological variables and S. We estimated that mean annual air and volume-weighted water temperatures increased by 0.028 and 0.033 °C year−1, respectively, from 1978 to 2011. Between 1986 and 1990, S and water temperature increased abruptly, probably due to a large upwards trend in air temperature (+0.239 °C year−1). We hypothesize that a mixing regime that lacked overturn took effect at this time and that this regime lasted until 2011, when S was particularly small. These results demonstrate that abrupt climate warming in the late 1980s likely triggered the termination of complete mixing and caused the 21-year period of successive anoxia in Lake Ikeda. We conclude that the lake response to a rapid shift in regional climate conditions was a key factor in changing the hypolimnetic water environment and that thermal stability in winter is a critical environmental factor controlling the mixing regime and anoxic conditions in deep lakes. Copyright © 2014 John Wiley & Sons, Ltd.