Thermal pollution reduces water quality through any process that leads to a change in the water’s ambient temperature. Karun is one of the most relevant sources of water supply in Iran, and its pollution, created by industrial, urban, and agricultural issues, has been one of the most critical challenges throughout the last few years. As the water temperature rises, the amount of dissolved oxygen in it decreases, thereby affecting the entire ecosystem associated with it. Drainage of urban and industrial runoff into surface water sources can increase the water temperature. Dams also constitute a significant part, modifying spatial patterns of temperature along river routes and causing thermal contamination. In this paper, the thermal pollution of the Karun River was assessed, and regions along this river with unusually raised water temperatures were identified and compared over 20 years. By analyzing the results, it can be found that the thermal pollution from dams has a significant impact on the downstream river environment and ecology that is considerably relevant during summer periods, showing average decreases of 3 degrees Celsius immediately beyond the dams’ locations (from 41 degrees Celsius upstream dams to 38 degrees Celsius beyond them) or even bigger (reductions of 13 degrees Celsius in one of the studied dams). Hence, our results showed that water temperature is colder downstream in the hot seasons of the year than upstream of the dams. The results suggest that the usage of remote sensing data effectively could complement collected data from ground-based sensors to estimate water temperature and to identify pollution areas. It provides experts with spatially extensive and highly synchronized data.