Most semi-enclosed seas have experienced severe eutrophication owing to high nutrient loading from rivers during rapid population growth periods. In Japan, the coastal areas of some megacities (e.g. Tokyo and Osaka) experienced considerable economic growth during the 1960s–1970s. Therefore, determining the amount of nutrient loading during this period is essential to undertake measures for the conservation of coastal environments. However, determining the nutrient loading that occurred several decades ago is generally difficult owing to lacking water quality records. In this study, the nitrogen loading in the Yamato River catchment, an urbanized coastal catchment in Asia, for 80 years from the 1940s to the 2010s is reconstructed using the Soil and Water Assessment Tool. We considered factors such as population growth, wastewater treatment plant (WWTP) construction, and changes in land and fertilizer usage in different urbanization stages. Results show that the total nitrogen loading in the catchment peaked in the 1970s at 6616 tons yr−1 owing to untreated wastewater discharge and rapid increase in population growth. By reducing 57% of the nitrogen loading in the 2010s from the catchment, WWTPs have been instrumental in improving the water environment. The decrease in and integration of agricultural land has reduced nitrogen loading attributed to nonpoint sources; however, this reduction was not obvious because of the high fertilizer usage before the 2000s. Overall, the findings of this study provide a comprehensive understanding of the impact of rapid urbanization in an Asian coastal catchment on nitrogen loading during the high economic growth period in the past. This study will be useful for the long-term assessment of nutrient loading in other.