The purpose of this study was to analyze the chemical water quality in the Youdeung Stream and compare fish tolerance, trophic guilds, community structure and the ecological health based on the Fish Assessment Index (FAI). Biochemical oxygen demand (BOD) and total phosphorus (TP) were the worst at the downstream sites, and overall, water quality tended to decline along with the longitudinal gradients from upstream to downstream. According to fish field survey, the number of fish sampled was 444 with were collected 31 species and the Zacco platypus was the dominant species. In addition, fish diversity declined toward the downstream, with an increase in tolerant species and a decrease in sensitive species. The significant increase in tolerant species in the downstream suggested the deterioration of the Youdeung Stream and the disturbance of the ecosystem based on the ecological health. Similar results have been derived from fish trophic guilds and the community structures which reflected the water chemistry of nutrients (N, P) and organic matter pollution. The ecological health, based on the FAI model, declined more in the downstream than the upstream. Fish compositions and trophic/tolerance guilds corresponded to the tendency of changes in the chemical water quality. Overall, the ecological health, based on the FAI model, were directly influenced by the chemical pollution in the stream.