Maintaining a certain number of spawning grounds for endangered fish is particularly important in rivers and streams where the environment changes drastically through floods and exploitations. Ryukyu-ayu Plecoglossus altivelis ryukyuensis is an endangered annual fish inhabiting the few streams and rivers flowing through the Amami-Oshima Island, southern Japan, and spawns in the lower reaches at sites with the specific riverbed conditions. In the island, resident volunteers along with researchers modify riverbed manually to provide conditions suitable for the natural spawning of the fish every year. This study investigated the effects of these activities on the riverbed conditions and consequently on the spawning by Ryukyu-ayu in two rivers. Our results showed that riverbed hardness and the amount of silt significantly decreased in the modified areas, but not in the adjacent unmodified areas. In one of the two rivers, the modification suppressed the settlement of net-spinning caddisfly larvae Stenopsyche schmidi that promote consolidation of the riverbed. The riverbed conditions in the modified areas were similar to those in the sites where P. a. ryukyuensis indeed spawned. These results suggest that manual modification is efficient in improving riverbed conditions for the spawning of Ryukyu-ayu. However, the eggs of the fish were not found at the modified areas in both rivers. It will be necessary to develop effective and practical ways of selecting sites for modification without obstructing the natural spawning in this fish.