The surface nutrient concentrations of the Northwest Pacific Ocean have shown distinct changes over the past four decades, which have been variably attributed to changes in anthropogenic nitrogen inputs or stratification. Here, we present a new data compilation that demonstrates a long-term decline in the surface nutrient concentrations caused by a significant decrease (∼25%) in the nutrient inventories of the permanent thermocline (100-850 m) rather than by enhanced stratification. This subsurface decrease is likely due to the northward expansion of high-temperature, low-nutrient subtropical gyre waters associated with climate change and a regional physical regime shift. Furthermore, a declining trend in the N:P ratio pointing toward greater N-limitation is observed in this research, in contrast to current assumptions inferring P-limitation by anthropogenic nitrogen inputs. Our results imply that these shifts may influence new production as well as carbon sequestration in this region.