Outputs from a high-resolution data assimilation system, the global Hybrid Coordinate Ocean Model and Navy Coupled Ocean Data Assimilation (HYCOM+NCODA) 1/12° analysis, were analyzed for the period September 2008 to February 2012. The objectives were to evaluate the performance of the system in simulating ocean circulation in the tropical northwestern Pacific and to examine the seasonal to interannual variations of the western boundary currents. The HYCOM assimilation compares well with altimetry observations and mooring current measurements. The mean structures and standard deviations of velocities of the North Equatorial Current (NEC), Mindanao Current (MC) and Kuroshio Current (KC) also compare well with previous observations. Seasonal to interannual variations of the NEC transport volume are closely correlated with the MC transport volume, instead of that of the KC. The NEC and MC transport volumes mainly show well-defined annual cycles, with their maxima in spring and minima in fall, and are closely related to the circulation changes in the Mindanao Dome (MD) region. In seasons of transport maxima, the MD region experiences negative SSH anomalies and a cyclonic gyre anomaly, and in seasons of transport minima the situation is reversed. The sea surface NEC bifurcation latitude (NBL) in the HYCOM assimilation also agrees well with altimetry observations. In 2009, the NBL shows an annual cycle similar to previous studies, reaching its southernmost position in summer and its northernmost position in winter. In 2010 and 2011, the NBL variations are dominantly influenced by La Niña events. The dynamics responsible for the seasonal to interannual variations of the NEC-MC-KC current system are also discussed.