Although the Onga River system is relatively small, it is home to three spined loach species, Cobitis takatsuensis, C . sp. ‘yamato’ complex, and C. striata (the Onga form of the middle race). The aim of the present study is to examine the relationship between the distribution pattern of the species and the physical parameters of the habitat. We mapped the distribution of these three species and measured six environmental factors at 86 points in this river system. Model selection was performed with a generalized linear model (GLM) using the AIC (Akaike’s Information Criterion) to find the best model for the distribution pattern of each species. The dependent variable was the presence/absence of each species, and the independent variables were six environmental factors. The environmental factors that had a positive effect were turbidity for C. takatsuensis, turbidity and river gradient for C. sp. ‘yamato’ complex, and turbidity, river gradient and width of dry riverbed for C. striata. In addition, the coexisting fish species also differ among the three loaches. These results revealed that the three spined loach species select particularly different habitats and can therefore coexist in this small river system.