In this study, a method was proposed for calculating the thermodynamic entropy increase ΔS in a water body after receiving excess discharge of organics and nutrients in order to quantitatively assess the impact of pollutants discharge on aquatic systems. The enthalpy change was evaluated using the standard thermodynamic data according to the possible chemical and/or biochemical reactions such as organic oxidation, nitrification/denitrification, and phosphorus precipitation, for the recovery of water quality to the background level. A series of equations were established for calculating the ΔS associated with the decomposition or removal of TOC, NO(3)-N, NO(2)-N, NH(3)-N and TP. The values of ΔS corresponding to unit mass (per g) of these pollutants were calculated as 54.0 kJ/K, 2.91 kJ/K, 10.01 kJ/K, 28.51 kJ/K and 2.81 kJ/K, respectively. Besides, the applicability of the proposed method was proved by a scenario analysis regarding effluent quality control and surface water quality protection in China.