The purpose of this study is to investigate effect of stream channel naturalness on ecological health by using environmental factors and Fish Assessment Index (FAI) in the Han River of South Korea. These samples and data have been released from the research project titled Stream/River Ecosystem Survey and Health Assessment, which was conducted in 444 sites in the Han river watershed from 2008 to 2016. All samples were classified into five groups according to a degree of morphological changes of stream. Water chemistry analyses indicated a decline in water quality by decreasing stream channel naturalness, it is assumed that channelized stream was vulnerable to aquatic pollution compared to the natural meandering stream. In the result of frequency of dominant species, sensitive species and insectivore such as Zacco koreanus, Rhynchocypris kumgangensis and Pungtungia herzi were frequently dominated in the natural meandering stream while tolerant species and omnivores such as Carassius auratus and Cyprinus carpio were more dominated in the channelized streams. The FAI in the channelized stream shows decline to average of 46±25 compared with that of the natural meandering stream (80±20). The decrease in FAI was highly influenced by changes in matrixes of fish assemblage structure such as number of sensitive species (M3), portion of omnivores (M5) and insectivores (M6). Moreover, annual average FAIs from 2008 to 2016 were significantly correlated with water chemistry, especially TN, TP and BOD (r²=0.59, p<0.0001). Taken together, all the results suggest that the stream channelization could negatively impact on the water quality and fish assemblage structure, leading to degradation in aquatic ecosystem health.