Water quality is one of the most essential factors to influence human daily life and environment health. Risk assessment of water quality has critical significance to sustainable development of human society and natural systems. Set pair analysis (SPA) methods are widely used in risk assessment, especially in water resources. The essence of SPA is to classify assessment samples consider the uncertainties exist in risk assessment system based on the viewpoints of unity, difference, and opposition. The existing SPA methods are classified into two types, including (i) original SPA and (ii) comprehensive SPA. Both the original and comprehensive SPA methods have the following limitations: (i) it is need to judge whether the assessment factor belongs to type I or type II; (ii) it is need to judge whether the assessment factor is positive or negative. This method article gives a detailed description of the application of the existing SPA method. The method article is a companion paper with the original article.