By contrast to the more regular and predictable temperate lakes, heat budgets and temperature dynamics in Mediterranean reservoirs are characterized by a marked interannual variability. In the present paper, the heat content, annual Birgean heat budget (ABHB), and thermal structure of Sau Reservoir were examined during a period of hypolimnetic withdrawal between 1980 and 1985, and during a period of withdrawal at intermediate depths between 1996 and 2003. The two study periods were also characterized by a wide range of stored water volume fluctuations. Results were used to develop and validate an empirical model to predict annual and monthly heat dynamics statistics and mixed layer depth as a function of hydraulic management parameters such as water volume and selective withdrawal depth. During the hypolimnetic withdrawal period elevated ABHB and deep mixed layer depths were recorded in the reservoir, which behaved as a heat trap. By contrast, intermediate depth withdrawal promoted a shallower and more stable thermocline, thus increasing the cold hypolimnetic water volume and decreasing heat content and ABHB. The study reveals that hydraulic management constitutes the main driver of the heat and thermal dynamics in reservoirs with multiple withdrawal outlets. By contrast with the increasing temperature trends recorded in many natural lakes, the hydraulic management in Sau Reservoir induced a progressive reduction in water temperature and heat content in the system, thus partially counteracting the possible deleterious effects of global warming. Our intensive study in a single, highly‐dynamic ecosystem constitutes a new approximation to the study of thermal structure and heat dynamics in water bodies.