Sea surface heights from the TOPEX/Poseidon altimeter are assimilated into a three-dimensional primitive equation model to derive the circulation in the South China Sea. With data assimilation the model resolves not only the basin-wide circulation but also a dipole off Vietnam and a low/high feature near the Luzon Strait. Mesoscale features are missing in the simulation without data assimilation because of poor resolution in the wind field and inadequate knowledge of the transport through the Luzon Strait. Compared to the case without data assimilation, data assimilation reduces the root mean square error between the simulated and observed sea surface heights by a factor of 2-3. Circulation derived from data assimilation under climatological conditions is contrasted with that during El Niño. In the normal winter of 1993-1994, flow at 50 m depth is strong and cyclonic. Flow at 900 m depth is cyclonic as well. The deep cyclone persists into the following summer. During the 1994-1995 El Niño winter, features in the flow field at 50 m depth either weaken or disappear, and circulation at 900 m depth is anticyclonic. In the summer of 1995 the dipole and the eastward jet off Vietnam at 50 m depth are missing, and the anticyclonic circulation at 900 m depth persists. Temperature at 65 m shows significant warming from fall 1994 to summer 1995. A weakened flow field and warming in the upper ocean are consistent with findings from earlier El Niño events.
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