An adjoint-free four-dimensional variational (a4dVar) data assimilation (DA) is implemented in an operational ocean forecast system based on an eddy-resolving ocean general circulation model for the Northwestern Pacific. Validation of the system against independent observations demonstrates that fitting the model to time-dependent satellite altimetry during a 10-day DA window leads to substantial skill improvements in the succeeding 60-day hindcast. The a4dVar corrects representation of the Kuroshio path variation south of Japan by adjusting the dynamical balance between amplitude/wavelength of the meander and flow advection. A larger ensemble spread tends to reduce the skill in representing the observed sea surface height anomaly, suggesting that it is possible to use the ensemble information for quantifying the forecast error. The ensemble information is also utilized for modification of the background error covariance (BEC), which improves the accuracy of temperature and salinity distributions. The modified BEC yields the skill decline of the Kuroshio path variation during the 60-day hindcast period, and the ensemble sensitivity analysis shows that changes in the dynamical balance caused by the ensemble BEC result in such skill deterioration.