Phosphorus usage is irreplaceable in agriculture; however, its excessive use leads to wastage of invaluable resources and significant soil surplus. Agronomic soil phosphorus surplus in Asian regions has a much higher level than the global average. And with rapid urbanization and population growth in recent decades, Asian countries have seen a rise in environmental pollution levels also. This study assessed the detailed phosphorus budget in the Yamato River catchment, an urbanized coastal catchment in Asia, from the 1940s to the 2010s using Soil and Water Assessment Tool, comprehensively analyzed the effect of anthropogenic factors on long-term phosphorus loading and agronomic soil phosphorus balance. The results showed the peak period of total phosphorus loading and agronomic soil phosphorus surplus occurred in the 1970s, at 895 tons/year and 36.6 kg/ha, respectively. The major reasons for increased phosphorus loading and soil surplus during 1940–1970 were rapid population growth and increased fertilizer usage, respectively. Since the 1980s, the construction of wastewater treatment systems and reduction in agricultural land contributed to environmental improvement. These anthropogenic factors had a much stronger impact on phosphorus budget than climate change in the study catchment. Soil phosphorus balance is affected by a combination of factors, such as soil properties, fertilizer usage and applied schedule, precipitation event, and crop types. And soil phosphorus surplus may be severely overestimated if the non-point source loss due to precipitation factor is not fully considered.