This study was to provide basic data for aquatic ecosystem research using fishes. Field sampling was carried out at five selected sites of Gap Stream, and fish samples, especially for a selection of sentinel species were collected three times in June, September, and October 2007. We analyzed total length distribution of Zacco platypus in relation with the season and the sampling sites, and then compared with total body weight, condition factor (K), and age distribution of the fish. The fish population data were compared with physico-chemical water quality, obtained from the Ministry of Environment, Korea. Water quality analysis showed a significant nutrient enrichment, based on total nitrogen (TN) and total phosphorus (TP), and organic matter pollution, based on biological oxygen demand (BOD) and chemical oxygen demand (COD) in the Site 5, which is directly influenced by wastewater disposal plant (WDP). Population analysis of the sentinel species showed that the total number of individuals, age distribution, and the population size-structure were influenced by the effluents from the WDP, and that reproductive failure of young-age population were evident in Site 5. According to the relation analysis of total weight to K, the disturbed population was mainly attributed to combined effects of habitat modifications and chemical degradations. Regression analysis of K values against water quality parameters showed significant (p<0.05) positive relations with nutrient and organic matter contents. Our data suggest that the population structure using a sentinel fish species reflected the ambient water quality in the stream and that diagnosis of aquatic ecosystem health using Z. platypus population may be practical for water resource and ecosystem conservations.