Heat uptake is a key variable for understanding the Earth system response to greenhouse gas forcing. Despite the importance of this heat budget, heat uptake by inland waters has so far not been quantified. Here we use a unique combination of global-scale lake models, global hydrological models and Earth system models to quantify global heat uptake by natural lakes, reservoirs, and rivers. The total net heat uptake by inland waters amounts to 2.6 ± 3.2 ×1020 J over the period 1900–2020, corresponding to 3.6% of the energy stored on land. The overall uptake is dominated by natural lakes (111.7%), followed by reservoir warming (2.3%). Rivers contribute negatively (-14%) due to a decreasing water volume. The thermal energy of water stored in artificial reservoirs exceeds inland water heat uptake by a factor ∼10.4. This first quantification underlines that the heat uptake by inland waters is relatively small, but non-negligible.