Extreme precipitation events, intensified by climate change, are increasingly disrupting nutrient dynamics in large river systems worldwide. Beyond altering the magnitude of individual nutrient fluxes, extreme precipitation may fundamentally reshape nutrient composition and stoichiometric balances, with critical implications for aquatic ecosystem health. Here, we apply an integrated data–model framework to assess how these events have altered nitrogen (N) and phosphorus (P) fluxes across the Mississippi River Basin from 1980 to 2018. We find that extreme rainfall disproportionately increases P export relative to N, driven primarily by enhanced soil erosion and mobilization of particulate-bound nutrients. Concurrent temporal and spatial changes in extreme precipitation regimes have induced declining N:P ratios in headwater streams and cumulative nutrient loads, shifting export stoichiometry toward the Redfield ratio. Therefore, extreme precipitation can increase nutrient fluxes that fuel harmful algal blooms, yet at the same time reduce N:P ratios that may favor less toxic communities. This trade-off calls for watershed management strategies that go beyond managing nutrient quantity alone.