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The objective of this study was to analyze chemical water quality, ecological characteristics of fish compositions and ecosystem health before (BWC, 2008-2009) and after (AWC, 2011-2012) at Juksan Weir and Seungchon Weir of Yeongsan River watershed. Suspended solids (SS) and Chlorophyll-a (Chl-a) in Juksan Weir increased, whereas nutrients such as total nitrogen (TN) and total phosphorus (TP) decreased in the epilimnetic water. According to fish species distribution analysis in the periods of BWC and AWC, both Juksan and Seungchon weirs showed that sensitive species were rare and tolerant species dominated the community. In the analysis of trophic guild, relative abundance of carnivore species increased 22% and 12%, respectively after the constructions of Seungchon Weir and Juksan Weir. Mann-Whitney U-tests of nonparametric statistical analysis indicated that omnivore and carnivore species had significant differences (p < 0.05) between the BWC and AWC. The massive population growth of exotic species, Micropterus salmoides, was evident in Seungchon Weir, thus influenced the structures of fish communities. The model values of mean Index of Biological Integrity (IBI), based on fish assemblages, were < 15, which indicates "poor” condition in the river health, and significant differences of IBI were not found between the BWC and AWC. Long-term fish monitoring is necessary to determine the magnitude of species compositions.