This study was conducted to select target fish species as baseline research for accumulation analysis of major hazardous chemicals entering the aquatic ecosystem in Korea and to analyze the impact on fish community. The test bed was selected from a sewage treatment plant, which could directly confirm the impact of the inflow of harmful chemicals, and the Geum River estuary where harmful chemicals introduced into the water system were concentrated. A multivariable metric model was developed to select target candidate fish species for hazardous chemical analysis. Details consisted of seven metrics: (1) commercially useful metric, (2) top-carnivorous species metric, (3) pollution fish indicator metric, (4) tolerance fish metric, (5) common abundant metric, (6) sampling availability (collectability) metric, and (7) widely distributed fish metric. Based on seven metric models for candidate fish species, eight species were selected as target candidates. The co-occurring dominant fish with target candidates was tolerant (50%), indicating that the highest abundance of tolerant species could be used as a water pollution indicator. A multi-metric fish-based model analysis for aquatic ecosystem health evaluation showed that the ecosystem health was diagnosed as “bad conditions”. Physicochemical water quality variables also influenced fish feeding and tolerance guild in the testbed. Eight water quality parameters appeared high at the T1 site, indicating a large impact of discharging water from the sewage treatment plant. T2 site showed massive algal bloom, with chlorophyll concentration about 15 times higher compared to the reference site.