This study attempts to estimate the value of the water quality improvement by deriving the equilibrium price of the water pollutant emission permit for the imaginary water pollutant emission trading market. It is reasonable to say that there is already an implicit social agreement for the unit value of water pollutant, when the government set the Total Water Pollutant Loading System for the major river basin as a part of the Comprehensive Measures for Water Management, particularly for the Nakdong River Basin. Therefore, we can derive the unit value of water pollutant emission, which is already implied in the pollution allowance for each city or county by the Total Water Pollutant Loading System. Once estimated, it will be useful to the economic assessment of the water quality related projects. An imaginary water pollutant emission trading system for the Nakdong River Basin, where Total Water Pollutant Loading System is already effective, is constructed for the estimation of the equilibrium price of water pollutant permit. By estimating marginal abatement cost curve or each city or county, we can compute the equilibrium price of the permit and then it is regarded as the economic value of the water pollutant. The marginal net benefit function results from the relationship between the emission and the benefit, and then the equilibrium price of permit comes from constructing the excess demand function of the permit by using the total allowable permit of the local government entity. The equilibrium price of the permit would be estimated to be $1,409.3won/kg{cdot}BOD$. This is within reasonable boundary compared for the permit price compared to foreign example. This permit price would be applied to calculate for the economic value of the water quality pollutants, and also be expected to use directly for the B/C analysis of the business involved with water quality change.