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Climate change impacts ocean nutrient availability and will likely alter the marine food web. While climate models predict decreased average ocean productivity, the extent of these changes, especially in the marginal seas upon which large human populations depend, is not well understood. Here, we reconstructed changes in seawater phosphate concentration and nitrate source over the past 400 years, which reveals a more than 50% decline in residence time of seawater phosphate, and 8%–48% decline in subsurface nitrogen supply following the coldest period of Little Ice Age. Our data indicates a link between surface ocean nutrient supply and the East Asian Summer Monsoon strength in an economically important marginal sea. As climate models predict that the East Asian Summer monsoon will strengthen in the future, our study implies that surface ocean primary productivity may increase in the South China Sea, contrary to the predicted decrease in global average ocean productivity. Plain Language Summary: Global climate models predict that surface ocean nutrient concentrations will significantly decrease over the next 100 years as our climate changes. However, in the world's marginal seas, which human populations depend on most heavily for food security, the surface ocean biogeochemical changes are still difficult to predict with global‐scale models. Here, using coral‐based paleoclimate proxies, we reconstruct changes to surface phosphate concentration and to sources of surface nitrogen over the past four centuries in the South China Sea (SCS). Combined with box model simulations, our data reveal a more than 50% decline in phosphate residence time and an 8%–48% decline in subsurface nitrate supply from the 1600s to present. Such a decline implies a significant decrease in primary productivity and likely a community shift toward nitrogen‐fixing phytoplankton. Importantly, our data indicate that the decrease in nutrient supply was driven by weakened monsoon‐induced upwelling, demonstrating strong ties between nutrient supply and monsoon strength in the SCS. Climate change is predicted to strengthen the East Asian Summer Monsoon, and our results suggest that primary productivity in this economically important region may increase, contrary to the widely predicted decreases in average global ocean productivity. Key Points: Coral skeletal phosphorus content with scattered nitrogen isotopes is reconstructed over the past 400 yearsNutrient supply declined up to 48% since the Little Ice Age in the western South China SeaThe coral record from links nutrient supply to monsoon wind, implying higher productivity under a stronger monsoon in the future [ABSTRACT FROM AUTHOR]