This study investigated fish communities at a total of 11 sites across four rivers in the region in 2005 and 2015. Sampling was conducted twice at each site using cast nets (10×10 mm mesh size) and scoop nets (4×4 mm and 5×5 mm mesh sizes). Basic water quality measurements and river naturalness assessments were also performed. Based on fish community survey results, a Self-Organizing Map (SOM) analysis was employed to evaluate the impact of urbanization on fish communities in the study area. The results revealed a tendency for decreased electrical conductivity in water quality and improved scores in river naturalness assessments. Compared to the environmental conditions in 2005, the overall naturalness of the study area appeared to have increased by 2015. A total of 721 individual fish representing 32 species from 12 families were collected. The dominant species was largemouth bass (Micropterus salmoides, 141 individuals, 19.6%), and the subdominant species was dark chub (Zacco temmincki, 132 individuals, 18.3%). The SOM analysis demonstrated a clear distinction in fish community distribution patterns between the survey years. Brackish water species such as Plecoglossus altivelis, Lateolabrax japonicus, and Mugil cephalus, along with introduced species like Erythroculter erythropterus, exhibited higher frequencies in 2015. Although the occurrence of exotic species tended to decrease compared to 2005, the presence of bluegill (Lepomis macrochirus) showed an increase in 2015. These findings suggest an increase in species favoring deeper waters and lacustrine environments, with notable growth in populations of introduced and exotic species.