Three ocean models, 1/25° global HYbrid Coordinate Ocean Model (HYCOM), 1/12° global HYCOM, and East Asian Seas Navy Coastal Ocean Model (EAS NCOM) nested in global NCOM, were used to provide a global context for simulation of the circulation within the Philippine Archipelago as part of the Philippine Straits Dynamics Experiment (PhilEx). The Philippine Archipelago provides two significant secondary routes for both the Indonesian throughflow and the western boundary current of the Pacific northern tropical gyre. The deeper route enters the archipelago from the north through Mindoro Strait, after passing through Luzon Strait and the South China Sea. The second route enters directly from the Pacific via the shallow Surigao Strait and passes through Dipolog Strait downstream of the Bohol Sea. Both pathways exit via Sibutu Passage and the adjacent Sulu Archipelago along the southern edge of the Sulu Sea, and both are deeper than the pathway into the Indonesian Archipelago via Karimata Strait in the Java Sea. Within the Philippine Archipelago, these pathways make the dominant contribution to the mean circulation and much of its variability, while their outflow contributes to the flow through Makassar Strait, the primary conduit of the Indonesian throughflow, at all depths above the Sibutu Passage sill. Because of the narrow straits and small interior seas, the simulations are very sensitive to model resolution (4.4 km in 1/25° global HYCOM, 8.7 km in 1/12° global HYCOM, and 9.6 km in EAS NCOM in this latitude range) and to topographic errors, especially sill depths. The model simulations for 2004 and 2008 (the latter the central year of the PhilEx observational program) show extreme opposite anomalous years with anomalously strong southward Mindoro transport in 2004 and mean northward transport in 2008, but with little effect on the Surigao-Dipolog transport. Satellite altimetry verified the associated HYCOM sea surface height anomalies in the western tropical Pacific and the South China Sea during these extreme years. A 15-month (December 2007–March 2009) PhilEx mooring in Mindoro Strait measured velocity nearly top to bottom at a location close to the sill. The 1/12° global HYCOM, which showed the strongest flow above 200 m lay west of the mooring, was used to adjust a Mindoro transport estimate from the mooring data for cross-sectional distribution of the velocity, giving 0.24 Sv northward over the anomalous observational period. The results from the observational period were then used to adjust the 2004–2009 model transport, giving a mean of 0.95 Sv southward. The 1/25° global HYCOM simulated the observed four-layer flow in Dipolog Strait and the vigorous and persistent cyclonic gyre in the western Bohol Sea, observed during all four PhilEx cruises and in ocean color imagery. This gyre was poorly simulated by the two models with ~ 9 km resolution. Finally, a 1/12° global HYCOM simulation with tides generated the hydrostatic aspect of the internal tides within the Philippine Archipelago, including a strong internal tidal beam initiated at Sibutu Passage and observed crossing the Sulu Sea.

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