The climatological water mass features, the seasonal variabilities of the thermohaline structure, and the linkage between fluxes (momentum, heat, and moisture) of the East China and Yellow Seas have been investigated. The long term mean surface heat balance corresponds to a heat gain of 15 W/m2 in the Yellow Sea shelf (YS), a heat loss of around 30 W/m2 in the East China Sea shelf (ECS) and Cheju bifurcation zone (CB), and around 65 W/m2 in the Taiwan Warm Current region (TWC) and Kuroshio Current region (KC). The surface fresh water balance, i.e., evaporation minus precipitation, ranges from -1.8 to -4.0 cm/ month for the five subareas. The four seasons for the stud area are divided based on the relative heat storage, which do not follow the usual atmospheric seasons. The entire water column of the ECS, YS and CB undergoes a seasonal thermal cycle with maximum values of temperature during summer and maximum mixed layer depths during winter. Only the surface waters of TWC and KC exhibit a seasonal thermal cycle. Two patterns exist in the surface salinity and Yangtze River run-off, out of phase in the East China Sea and in phase in the Yellow Sea.