The construction of dams, weirs, irrigation infrastructure and regulators impact 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 between 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 Peryaja Irrigation Dam on the Komering River (Sumatra island) and another on Poso Dam on the Poso River (Sulawesi island). Neither of these structures have been assessed and many other projects are proceeding without considering potential fisheries impacts. The proposed infrastructure upgrades over the next two decades provides a once-in-a-generation opportunity to ensure that migratory fish are adequately protected from infrastructure projects. But there is an urgent need to collect and apply ecological and hydrological criteria to develop functional fish pass designs. A research for development approach where new information is applied, in an adaptive sense, to new projects will protect fisheries resources which form a source of food and livelihoods for many.