Protected areas maintain neotropical freshwater bird biodiversity in the face of human activity

•It is unclear whether land protection works as a tool to conserve freshwater animal assemblages.•We compared freshwater bird richness and abundance in lakes within and outside protected areas.•Compared to other ecological factors, land protection was a strong predictor of bird abundance.•Neotropical protected areas may be effective in maintaining freshwater bird biodiversity. Because of their accessibility, freshwater ecosystems are particularly sensitive to deforestation and bank habitat fragmentation. Their responses to human activities in general, and specifically to small-scale extractive activities, are not well understood. Protected Areas (PAs) can be an effective tool to secure the conservation of freshwater animal assemblages. Given their ability to respond to changes in site quality and local resources, waterbirds could be suitable wetland ecosystem indicators. To examine the effectiveness of PAs in protecting neotropical biodiversity, we used repeated visual count surveys of freshwater and forest-associated birds, comparing species richness and abundance in protected oxbow lakes with lakes subject to gold mining and fishing activities. Bird community structure was predicted by the proportion of mined area in lake banks and water quality. Bird richness was reduced in unprotected oxbow lakes, and this pattern was stronger for aquatic species. Land protection was the most important predictor of bird abundance. Over half the species (53%) showed markedly reduced abundance in the unprotected sites. Our results provide evidence for the effectiveness of PAs in maintaining freshwater biodiversity and for the impacts of human activities on neotropical wetland bird assemblages. Our findings also suggest that water-associated species may be sensitive to the deterioration in hydrological processes promoted by these activities. By documenting the maintenance of elevated freshwater bird biodiversity within two PAs, our results inform the debate on their effectiveness. We recommend the extension of legal protections for freshwater ecosystems and their banks to prevent further degradation of essential habitats and animal communities, driven by expanding informal and illegal mining activities.