Water quality modeling is an ideal tool for simulating physical, chemical, and biological changes in aquatic systems. It has been utilized in a number of GIS-based water quality management and analysis applications. However, there is considerable need for a decision-making process to translate the modeling result into an understandable form and thereby help users to make relevant judgments and decisions. This paper introduces a water quality index termed QUAL2E water quality loading index (QWQLI). This new WQI is based on water quality modeling by QUAL2E, which is a popular steady-state model for the water quality of rivers and streams. An experiment applying the index to the Sapgyo River in Korea was implemented. Unlike other WQIs, the proposed index is specifically used for simulated water quality using QUAL2E to mainly reflect pollutant loading levels. Based on the index, an iterative modeling-judgment process was designed to make decisions to decrease input pollutants from pollutant sources. Furthermore, an indexing and decision analysis can be performed in a GIS framework, which can provide various spatial analyses. This can facilitate the decision-making process under various scenarios considering spatial variability. The result shows that the index can evaluate and classify the simulation results using QUAL2E and that it can effectively identify the elements that should be improved in the decision-making process. In addition, the results imply that further study should be carried out to automate algorithms and subsidiary programs supporting the decision-making process.