Dissolved inorganic phosphorus (DIP) concentrations in the oligotrophic surface waters of the South China Sea decrease from ∼20 nM in March 2000 to ∼5 nM in July 2000, in response to seasonal water column stratification. These minimum DIP concentrations are one order of magnitude higher than those in the P‐limited, iron‐replete stratified surface waters of the western North Atlantic, suggesting that the ecosystem in the South China Sea may be limited by bioavailable nitrogen or some trace nutrient rather than DIP. Nutrient enrichment experiments using either nitrate, phosphate or both indicate that nitrogen limits the net growth of phytoplankton in the South China Sea, at least during March and July 2000. The fixed nitrogen limitation may result from the excess phosphate (N:P<16) transported into the South China Sea from the North Pacific relative to microbial population needs, or from iron control of nitrogen fixation. The iron‐limited nitrogen fixation hypothesis is supported by the observation of low population densities of Trichodesmium spp. (<48 × 103 trichomes/m3), the putative N2 fixing cyanobacterium, and with low concentrations of dissolved iron (∼0.2–0.3 nM) in the South China Sea surface water. Our results suggest that nitrogen fixation can be limited by available iron even in regions with a high rate of atmospheric dust deposition such as in the South China Sea.

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Up to 2 μM of nitrate anomaly, N*, were found in the upper nutricline at the South East Asia Time‐series Study (SEATS) site in the northern South China Sea (SCS). These concentrations were among the higher values reported in the Pacific and indicate the significant contribution of the remineralization of nitrogen‐rich organic matter formed by nitrogen fixation to the nutrient dynamics of the area. The concentrations were systematically higher, by up to 2.5 μM, in the Fall through the early Spring, during the northeast monsoon, than in the Summer, suggesting that the impact of nitrogen fixation was higher during the former time period. This pattern is in phase with that of the atmospheric deposition of Asian dust to the northern SCS. The coherence is consistent with a coupling between nitrogen fixation and the availability of atmospherically derived iron.