The lower Ebro River (Spain) is subject to the thermal and hydrological alterations caused by the system of reservoirs of Mequinenza, Riba‐roja, and Flix and to the thermal effluent of the nuclear power plant of Ascó, located 5 km downstream from the three reservoirs. In this paper, a modeling approach is used to determine the equilibrium temperature and recuperation distance at the study reach for different seasons and hydrological years. The intensity of the alteration caused by the reservoirs and nuclear power plant effluent is studied in reference to the equilibrium temperature and discharge rate. Mean daily water temperature downstream from the reservoirs is higher than mean daily equilibrium temperature in the fall and is lower during the rest of the year. Changes in the heat fluxes induced by thermal alteration are also addressed, showing important variations in evaporation and conduction to the atmosphere.