In recently decades, many coastal waters have experienced serious eutrophication due to rapid increase in nutrient fluxes in the coastal watersheds. Therefore, understanding the nutrient budget in the watershed-coastal water consortium is essential for effective coastal management. A coupled model consists of watershed model (SWAT) and ocean model with water quality module (ECOMSED + WASP5) was developed to investigate nitrogen budget on seasonal and annual timescales for the Han River Watershed (HRW) -Han River Estuary (HRE) consortium near the Taiwan Strait (TWS). Results showed that wet-season rainfall drove substantial nitrogen loss in the HRW, where nitrate leaching became the dominant nitrogen sink, accounting for approximately 36 % of the total nitrogen loss. Nitrogen retention rate in the HRW was about 80 %, and the other 20 % was transported to the HRE by runoff. The horizontal distributions of dissolved inorganic nitrogen (DIN) and organic nitrogen (ON) in the HRE generally followed the river plume and coastal currents. Nitrogen budgets in the HRE were dominated by physical processes while biogeochemical processes further regulated it. In summer, the nitrogen in the HRE mainly contributed by shelf upwelling, followed by riverine input; in the non-summer season, the nitrogen in the HRE was mainly contributed by the Zhe-Min Coastal Waters. In addition, the riverine DIN input was important in sustaining nitrogen cycling of the HRE. These findings highlight the need for seasonally adaptive management strategies for the HRE and its’ coastal waters, and demonstrates the importance of integrated watershed-coastal ocean modeling for effective eutrophication control in rapidly developing regions.