The purpose of this study is to suggest improvements of Eco-Natural map preparation guideline by presenting assessment methods that can be applied to the result of river ecosystem health survey and assessment, using the Geographic Information System. The area for studying is the main stream of the Hwang River where is easy to collect data and available to compare before and after of river assessment. It was reevaluated by reflecting the result of river ecosystem health assessment of the Ministry of Environment. As the result, Eco-Natural map of the study area reflecting the river assessment, the changes in the area ratio by grade have been increased from 1.14% to 14.03% in the first-grade and from 24.64% to 43.91% in the second-grade. It is considered to present more realistic grade due to the assessment of the rivers that have not been reflected in the meantime. Consequently, the result of this study will be useful for establishing the development projects on the rivers, providing the foundation for more realistic and active protection.