Animal migrations transport resources among spatially separate ecosystems, effectively linking them. In freshwater ecosystems, numerous fish species migrate between mainstream rivers or lakes and their tributaries, providing resources and nutrients during their spawning migrations. Multiple migratory species travel to the same destinations and contribute such nutrients, but knowledge remains limited about how the diversity of migratory animals influences the recipient ecosystem. We investigated how migrations of diverse fish community from Lake Biwa, Japan contribute to nutrient inputs in one of the lake’s tributary rivers and how they influence the ecosystem. Sequential migration of six fish species continued for 8 months of a year, causing high-level nutrient concentration and primary production. The fish-derived resources were taken up by diverse members of the river community. Our results emphasize the extent to which migrations of diverse animals seasonally extend and stabilize the resource subsidy and how they extend pronounced effects on the recipient ecosystems.