The (Lower) Lake of Zurich provides an ideal system for studying the long-term impact of environmental change on deep-water hypoxia because of its sensitivity to climatic forcing, its history of eutrophication and subsequent oligotrophication, and the quality and length of its data set. Based on 39 years (1972-2010) of measured profiles of temperature, oxygen concentration and phosphorus (P) concentration, the potentially confounding effects of oligotrophication and climatic forcing on the occurrence and extent of deep-water hypoxia in the lake were investigated. The time-series of Nürnberg's hypoxic factor (HF) for the lake can be divided into three distinct segments: (i) a segment of consistently low HF from 1972 to the late-1980s climate regime shift (CRS); (ii) a transitional segment between the late-1980s CRS and approximately 2000 within which the HF was highly variable; and (iii) a segment of consistently high HF thereafter. The increase in hypoxia during the study period was not a consequence of a change in trophic status, as the lake underwent oligotrophication as a result of reduced external P loading during this time. Instead, wavelet analysis suggests that changes in the lake's mixing regime, initiated by the late-1980s CRS, ultimately led to a delayed but abrupt decrease in the deep-water oxygen concentration, resulting in a general expansion of the hypoxic zone in autumn. Even after detrending to remove long-term effects, the concentration of soluble reactive P in the bottom water of the lake was highly correlated with various measures of hypoxia, providing quantitative evidence supporting the probable effect of hypoxia on internal P loading. Such climate-induced, ecosystem-scale changes, which may result in undesirable effects such as a decline in water quality and a reduction in coldwater fish habitats, provide further evidence for the vulnerability of large temperate lakes to predicted increases in global air temperature.