Rivers provide unrivaled opportunity for clean energy via hydropower, but little is known about the potential impact of dam-building on the food security these rivers provide. In tropical rivers, rainfall drives a periodic flood pulse fueling fish production and delivering nutrition to more than 150 million people worldwide. Hydropower will modulate this flood pulse, thereby threatening food security. We identified variance components of the Mekong River flood pulse that predict yield in one of the largest freshwater fisheries in the world. We used these variance components to design an algorithm for a managed hydrograph to explore future yields. This algorithm mimics attributes of discharge variance that drive fishery yield: prolonged low flows followed by a short flood pulse. Designed flows increased yield by a factor of 3.7 relative to historical hydrology. Managing desired components of discharge variance will lead to greater efficiency in the Lower Mekong Basin food system.