The estimation of manure phosphorus loss (MPL) in runoff is crucial for addressing environmental problems linked to nonpoint source pollution. Using a data-driven model, we assessed MPL in 520 major global river basins for the year 2000. Global mean MPL was 1.6 kgP/ha with a median of 0.9 kgP/ha. Hotspots were identified in the basins of South and Southeast Asia, Northwestern Europe, and South America. Importantly, 26% of basin areas showed high uncertainty due to input data, while approximately 43% exhibited low uncertainty. Continental analysis highlighted large uncertainties in Asia and South America, particularly in the Amazon, Ganges, Yangtze, and Nile basins, compared to Europe and the eastern United States. Our findings uncovered substantial uncertainties, even with a simple model, suggesting that more complex models can exacerbate uncertainties and lead to misinterpretations. Thus, there is a need for enhanced data quality and recognition of the conditional nature of model-based estimates.