Within the last decades, the water temperature of several European lakes has risen. It is assumed that these temperature increases are due to a reconfiguration of the heat-balance components. This study explores the dominant modifications of heat exchange with the atmosphere and their temporal evolutions. The objective is to identify the primary changes in heat fluxes and the sequence of events of the reconfiguration for the period 1984–2011. For this purpose, a model was applied to Lake Constance to estimate the contributions of the individual heat fluxes to the total heat balance. The results show that increasing absorption of solar radiation (+0.21 ± 0.13 W m−2 yr−1) and of longwave radiation (+0.25 ± 0.11 W m−2 yr−1) was responsible for the lake surface warming of 0.046 ± 0.011°C yr−1. Heat losses to the atmosphere by longwave emission (−0.24 ± 0.06 W m−2 yr−1) and by latent heat flux (−0.27 ± 0.12 W m−2 yr−1) have intensified in parallel due to higher lake surface temperatures. The heat budget is in a quasi-steady state, whereas incoming solar radiation and the warmer atmosphere increased the lake surface temperature; the warmer surface emits more longwave radiation and more water is evaporated. At each level of the slowly increasing water temperature, the heat fluxes are balanced. The overall change of the total heat content, however, is relatively little. Although the cooling effect of inflowing rivers decreased, this contribution is also small.