The quantified analysis of damages to wastewater treatment plants by natural disasters is essential to maintain the stability of wastewater treatment systems. However, studies on the quantified analysis of natural disaster effects on wastewater treatment systems are very rare. In this study, a total disaster index (DI) was developed to quantify the various damages to wastewater treatment systems from natural disasters using two statistical methods (i.e., AHP: analytic hierarchy process and PCA: principal component analysis). Typhoons, heavy rain, and earthquakes are considered as three major natural disasters for the development of the DI. A total of 15 input variables from public open-source data (e.g., statistical yearbook of wastewater treatment system, meteorological data and financial status in local governments) were used for the development of a DI for 199 wastewater treatment plants in Korea. The total DI was calculated from the weighted sum of the disaster indices of the three natural disasters (i.e., TI for typhoon, RI for heavy rain, and EI for earthquake). The three disaster indices of each natural disaster were determined from four components, such as possibility of occurrence and expected damages. The relative weights of the four components to calculate the disaster indices (TI, RI and EI) for each of the three natural disasters were also determined from AHP. PCA was used to determine the relative weights of the input variables to calculate the four components. The relative weights of TI, RI and EI to calculate total DI were determined as 0.547, 0.306, and 0.147 respectively.