Changes in heat energy stored within a column of wetland surface water can be a considerable component of the surface energy budget, an attribute that is demonstrated by comparing changes in stored heat energy to net radiation at seven sites in the wetland areas of southern Florida, including the Everglades. The magnitude of changes in stored heat energy approached the magnitude of net radiation more often during the winter dry season than during the summer wet season. Furthermore, the magnitude of changes in stored heat energy in wetland surface water generally decreased as surface energy budgets were upscaled temporally. A new method was developed to estimate changes in stored heat energy that overcomes an important data limitation, namely, the limited spatial and temporal availability of water temperature measurements. The new method is instead based on readily available air temperature measurements and relies on the convolution of air temperature changes with a regression‐defined transfer function to estimate changes in water temperature. The convolution‐computed water temperature changes are used with water depths and heat capacity to estimate changes in stored heat energy within the Everglades wetland areas. These results likely can be adapted to other humid subtropical wetlands characterized by open water, saw grass, and rush vegetation type communities.