AbstractClimate 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.