Microplastics (MPs) remain in the aquatic environment for long periods due to their persistence, and there are concerns that they may adversely affect aquatic ecosystems. On the other hand, there is the problem that the number of research cases on MPs for aquatic organisms has been limited in Japan. In this study, we aimed to understand the actual presence of MPs in the digestive tract of freshwater fish and the relationship between MPs in the digestive tract of fish and their habitat. In the survey of MPs in the digestive tract of Gnathopogon elongatus elongatus, there was a significant difference in the number of MPs between the June and October samples, suggesting the effect of activation of its feeding behaviour during the breeding season. In the survey of MPs in the sediment, Polyester fibers were the most abundant MPs in the sediment, suggesting that fibrous MPs sourced from laundry wastewater flow into the Shokanji River and Shokanji Pond and are deposited in the sediment environment. Comparison of the components of MPs in the digestive tract of G. elongatus elongatus and MPs in the sediment indicated that it also ingests MPs present in the sediment when preying on benthic organisms.