Surface height fluctuations across an eastward flowing boundary current, such as the Gulf Stream and the Kuroshio, can be caused by changes both in the upstream inflow and in the neighboring recirculation gyres. Clarifying these causes is important in understanding the time-dependent nature of the boundary currents and their relationship to the surface wind and buoyancy forcing. Using satellite altimetry data to identify these causes, however, requires mean surface height field information, which is not readily available from the altimetry observation owing to lack of accurate geoid data. The present study presents a method to estimate the mean surface height profile across a boundary current system (including recirculation gyres) by combining altimetrically measured residual height data and historical hydrographic data. Applying this method to the Kuroshio revealed that the absolute surface height profiles thus estimated agree well with the results from quarterly, in-situ hydrographic observations. By separating the signals of the surface height fluctuations into those of the eastward flowing jet and the recirculation gyres, we found that the seasonal cycle in the surface transport of the Kuroshio, which has a maximum in July and August, is primarily due to the seasonal change in the intensity of the recirculation gyre south of the Kuroshio.