Tropical rivers have high annual discharges optimal for hydropower and irrigation development. The Mekong River is one of the largest tropical river systems, supporting a unique mega-diverse fish community. Fish are an important commodity in the Mekong, contributing a large proportion of calcium, protein, and essential nutrients to the diet of the local people and providing a critical source of income for rural households. Many of these fish migrate not only upstream and downstream within main-channel habitats but also laterally into highly productive floodplain habitat to both feed and spawn. Most work to date has focused on providing for upstream fish passage, but downstream movement is an equally important process to protect. Expansion of hydropower and irrigation weirs can disrupt downstream migrations and it is important to ensure that passage through regulators or mini hydro systems is not harmful or fatal. Many new infrastructure projects (<6 m head) are proposed for the thousands of tributary streams throughout the Lower Mekong Basin and it is important that designs incorporate the best available science to protect downstream migrants. Recent advances in technology have provided new techniques which could be applied to Mekong fish species to obtain design criteria that can facilitate safe downstream passage. Obtaining and applying this knowledge to new infrastructure projects is essential in order to produce outcomes that are more favorable to local ecosystems and fisheries.