Measurements of the thermal stratification at 3 locations within Fathom Five National Marine Park in Lake Huron, Ontario during the summers of 2006 and 2007 found large oscillations in the position of the thermocline. These oscillations led to considerable variability in the temperature at a given depth, with frequent changes in temperature at a rate of 5 °C per hour, and brief periods where temperatures changed at the rate of 10 °C per hour. The thermal stress due to such fast rates of temperature change has been previously implicated in negative effects on many aquatic organisms. The thermocline was observed to move by as much as 20 m vertically, and had dominant periods of oscillation of 12, 17 and 24 h. The strongest temperature variability occurs in the depth range of 10–20 m, which accounts for 20% of the total lakebed area within Fathom Five. The temperature variability was lowest in deep regions well below the thermocline and at a sheltered area behind a reef. This variability was a ubiquitous feature of the water column of Fathom Five during the summer stratification, and the impact of these frequent short-term thermal fluctuations on benthic and fish habitat is discussed in this note.