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Advocating proper phosphorus (P) fertilisation is necessary to save this limited natural resource and to save the investment in rice cultivation. This study aimed to evaluate changes in phosphorus availability, total phosphorus in soil, phosphorus buffering capacity, and phosphorus saturation in the long-term phosphorus fertilisation in the paddy rice system. Soil samples were collected in the harvest stage after seven consecutive crops over three years at Can Tho city, Vietnam. The applied phosphorus fertiliser rates were: no phosphorus fertilisation (P0), 17.4 kg P/ha (P17.4), and 26.2 kg P/ha as farmer's practice (P26.2). The results showed that the soil phosphorus buffering capacity in P0, P17.4 and P26.2 treatments was 9.49, 9.08 and 9.04 mg/kg, respectively. The degree of phosphorus saturation of P17.4 and P26.2 treatments ranged from 17.7% to 25.5%, showing the medium to high risk of phosphorus leaching. This study indicated that the application of phosphorus rate higher than 17.4 kg P/ha might result in the reduced soil phosphorus buffering capacity in the intensive rice cropping system in the Vietnamese Mekong Delta region. Our results implied that the application of a rate lower than 17.4 kg P/ha/crop could be extended to the other rice-growing (double/triple rice) areas in the Vietnamese Mekong Delta region or other paddy rice on alluvial soils in Asia.