Seasonal variations in the upper water column of the western North Pacific are simulated with the Regional Ocean Model System (ROMS). The model is driven by surface fluxes of heat, momentum and freshwater without prescribing sea surface temperature or salinity. A series of numerical experiments are conducted to explore the sensitivity of the upper ocean thermal structure to the parameterized solar penetration scheme and two common practices to control model climate through a flux correction term and a nudging term. The absorption of solar radiation by the water column beneath the sea surface destabilizes the upper layers to cause a stronger mixing and deeper mixed layer in the warm season (from April to September). Therefore, removing solar penetration from the model results in an exceptionally stable surface layer, and tends to produce an overly shallow mixed layer in the warm season. The experiment with a prescribed net surface heat flux shows that the model is unable to maintain a heat balance in the upper water column, producing a cooling trend. Experiments with a flux correction term are able to keep the simulated sea surface temperature (SST) from a long term drift by adjusting the amount of the net surface heat flux. However, unrealistic net surface heat flux is produced in the experiment, when the model assumes no solar penetration. The implementation of a weak temperature nudging (1/50 days) toward a long term mean climatology prevents the model from simulating a cold bias during long term integration. The experiment with solar penetration and a weak nudging produces reasonable interannual variability during the period of 1995 - 2006 without flux corrections. The nudging terms steer advective heat fluxes towards the climatological mean state so as to avoid long-term drift in upper water column heat content. A detailed understanding of the function of nudging terms in controlling the hydrodynamics of the water column remains to be investigated.