Nutrient enrichment and climate warming threaten freshwater systems. Metabolic theory and the paradox of enrichment predict that both stressors independently can lead to simpler food-webs having fewer nodes, shorter food-chains and lower connectance, but cancel each other's effects when simultaneously present. Yet, these theoretical predictions remain untested in complex natural systems. We inferred the food-web structure of 256 lakes and 373 streams from standardized fish community samplings in France. Contrary to theoretical predictions, we found that warming shortens fish food-chain length and that this effect was magnified in enriched streams and lakes. Additionally, lakes experiencing enrichment exhibit lower connectance in their fish food-webs. Our study suggests that warming and enrichment interact to magnify food-web simplification in nature, raising further concerns about the fate of freshwater systems as climate change effects will dramatically increase in the coming decades.