Alluvial fans, located near mountainous regions, are characterised by substantial sediment supply, large variations in flow and significant disturbances. The river channels on alluvial fans support a distinct biological community compared to those on alluvial plains. In Japan, gravel extraction and riverbed dredging to maintain flood discharge capacity were frequently carried out during the rapid economic growth period of the 1960s, leading to significant human impact on these rivers. As a result of frequent disturbances, the fish communities in these rivers tend to be less diverse. Furthermore, research on river channels in alluvial fans is limited compared to that on alluvial plains, resulting in a lack of detailed information on these ecosystems. Consequently, efforts for ecosystem conservation and restoration in these environments are insufficient. A fish survey was conducted at a total of 26 sites across four river channels on alluvial fans, each with distinct geological characteristics. The results revealed the presence of 2,265 individuals belonging to 15 species and one genus (only the genus could be identified) within seven families. Amongst the confirmed species were Misgurnus anguillicaudatus (Cantor, 1842), Oncorhynchus masou ishikawae (Jordan and McGregor, 1925) and Cottus pollux Günther, 1873, all of which are listed in the local Red Data Book, highlighting the presence of rare species even in river channels on alluvial fans impacted by human activity. Furthermore, non-native species were found only at a single site in the upstream section, where four individuals of Oncorhynchus mykiss (Walbaum, 1792) were collected. The survey indicated that species diversity and fish species composition varied across the different rivers, suggesting that various factors, such as watershed geology, geomorphological processes and anthropogenic influences, contribute to differences in fish community structure.