Understanding change through time in dissolved oxygen (DO) in lakes requires the use of long-term historical monitoring data. The data contained herein include historical temperature and dissolved oxygen profiles from two Swiss lakes collected between the years 1972 to 2017. These two lakes are a subset of a larger set of lakes that were used to examine the relationship between long-term changes in the timing of lake stratification and changes in the amount of oxygen-depleted water present in the water column.