To gain a better understanding of the geochemical behavior of trace elements in estuary and to examine seasonal variations in associated chemical fluxes, more than 50 water samples were collected near the mouth of the Gaoping (formerly spelled Kaoping) River, a major river in southwestern Taiwan. These samples, collected in typical dry and wet tropical monsoon seasons during 1999–2004, were analyzed for dissolved major and trace elements and Sr isotopes. Our results show that dissolved Na, Mg, Ca and Cl behave conservatively along the salinity gradient and display significantly larger fluxes in the wet seasons. Vertical profiles of the major elements reveal mainly two end-member mixing between the riverine freshwater and the seawater. Trace elements of B, Sr and U also display conservative distribution in the vertical profiles. In contrast, dissolved Ba and Mn were affected by uptake/release processes involving groundwater, benthic flux and water/sediment interactions. 87Sr/86Sr ratios also support a scenario of mixing between a more radiogenic continental source and the seawater. It appears that the wet season samples have higher trace element concentrations due to inputs from topsoils and atmospheric dusts. This implies that chemical compositions in river waters respond sensitively to regional climatic changes. The observed high fluxes of B and Sr in the Gaoping (Kaoping) River emphasize the potential impact of mountainous rivers on the global oceanic mass balance of these constituents.