The objectives of study were to evaluate fish species compositions of trophic guilds and tolerance guilds and apply ecological fish assessment (EFA) models to Bekjae Weir, Keum-River Watershed. The EFA models were Stream Index of Biological Integrity (SIBI) used frequently for running water and Lentic Ecosystem Health Assessment (LEHA) used for assessments of stagnant water. The region of Bekjae Weir as a "four major river project" was originally a lotic ecosystem before the weir construction (2010, BWC) but became more like lentic-lotic hybrid system after the construction (2011, AWC). In the analysis of species composition and ecological bioindicator (fish), fish species with a preference of running water showed significant decreases (p < 0.05), whereas the species with a preference of stagnant water showed significant increases (p < 0.05). After the weir construction, relative abundances of tolerant species increased, and the proportion of insectivores decreased. This phenomenon indicated the changes of biotic compositions in the system by the weir construction. Applications of SIBI and LEHA models to the system showed that the two model values decreased at the same time after the weir construction (AWC), and the region became more like lentic-lotic hybrid system, indicating the degradation of ecosystem health. The model values of SIBI were 19 and 16, respectively, in the BWC and AWC, and the health conditions were both "C-rank". In the mean time, the LEHA model analysis showed that the values was 28 in the BWC and 24 in the AWC, thus the health was turned to be "B-Rank" in the BWC and "C-Rank" in the AWC. indicating a degradation of ecological heath after the weir construction.