Populations of migratory waterbirds are facing dramatic declines worldwide due to illegal hunting, habitat loss and climate change. Conservation strategies to reverse these trends are imperative, especially in tropical developing countries, which almost invariably allocate insufficient levels of investment for environmental protection. Here, we compared the effectiveness of sustainable-use Protected Areas (PAs) and Community-based Conservation (CBC) arrangements for the conservation of migratory waterbirds that breed on seasonal riverine sandy beaches in Brazilian Amazonia. We modeled local population responses of four migratory waterbird species on 155 beaches along a ~1,600 km section of a major tributary of the Amazon, as a function of community enforcement, official protection status, human pressure and landscape features. We show that 21 community-protected beaches within the study area host more than 80% of all sampled birds. Black Skimmers showed the most dramatic response, with breeding numbers 135-fold larger in CBC arrangements compared to beaches with no official protection status. The same pattern was observed for nesting Large-Billed and Yellow-Billed Terns. For the Near Threatened Orinoco Goose, PA status was the strongest predictor of local population size. These dramatic results demonstrate the value of protected refugia, achieved through the concerted action of participating local communities, to support breeding populations of key waterbird species. This highly-effective and low-cost conservation model can potentially be replicated in other regions of the developing world experiencing increasingly intensive exploitation of riverine natural resources.