The habitats of aquatic organisms, including freshwater fishes (Oncorhynchus masou masou, Plecoglossus altivelis altivel, and Cyprinus carpio), fireflies (Luciola cruciata and Luciola lateralis), and frogs (Anura sp.), were evaluated dynamically in the Natori River basin in the central Miyagi prefecture in Japan using water temperature as an environmental index. The HSI (habitat suitability index) and WUA (weighted useable area) of aquatic organisms were quantitatively calculated using a distributed runoff model coupled with a heat budget model, land cover data, and digital cartographic data. The results showed that the HSI values of O. masou masou and P. altivelis altivel tended to be high in locations where they were actually observed. The HSI distribution patterns of L. cruciata and L. lateralis showed different results, even though the two species are in the same genus and have similar life cycles. The HSI distribution of Anura sp. returned an average value for the whole basin except for urban and upstream basin areas. In fact, Anura sp. frogs were observed throughout the study basin. Incorporating the dynamic factor of water temperature in the model allowed for monthly evaluations, especially for annual migratory organisms, such as P. altivelis altivel. WUA fluctuations, considering river water temperature, can characterize the annual behavior of P. altivelis altivel and Anura sp., and the partial behavior of O. masou masou.