Development activities threaten the long-term sustainability of tropical floodplain systems. The construction of dams, weirs, irrigation infrastructure and regulators affect connectivity among habitats and can facilitate rapid declines in riverine biota, especially fish. Indonesia is a tropical island country with an abundance of monsoonal rivers. Massive expansions in hydropower and irrigation infrastructure are planned over the next two decades and mitigation measures will be needed to protect migratory fish. Most Indonesian freshwater fish need to migrate among habitats to complete essential life-history stages. So, strategies are urgently needed to mitigate the barrier effects of river infrastructure to ensure the long-term sustainability of river fishes. A common tool used worldwide is the construction of upstream and downstream fish passes. Only two fish passes exist in Indonesia. One at Perjaya Irrigation Dam on the Komering River (Sumatra island) and another on Poso Dam on the Poso River (Sulawesi island). Neither of these structures has been assessed and many other projects are proceeding without considering potential impacts on fisheries. The proposed infrastructure upgrades over the next two decades provide a once-in-a-generation opportunity to ensure that migratory fish are adequately protected into the future.