The loss of nitrogen (N) and phosphorus (P) via surface runoff induced by fertilisation leads to water pollution and aggravates water scarcity. Studies estimating N and P losses from farmland have focused on the efficacy of agricultural management actions at reducing the amount of N and P lost. However, a gap remains in understanding the dynamics of N and P losses from farmland, especially differences among types of farmland, crop and fertiliser. Thus, the temporal variations of N and P losses via surface runoff from farmland induced by fertilisation were estimated using 5530 groups of paired observations collected in China. The results showed that N and P losses via surface runoff from paddy fields associated with fertilisation were greater than losses from upland fields. However, after > 90 days post-fertilisation, the effects of fertilisation on N and P loss from paddy fields were non-significant, while the effects of fertilisation on N and P losses from upland fields remained significant. Organic fertilisation decreased N losses from upland and paddy fields, but at more than 60 days post-fertilisation, N and P losses from upland fields were greater with organic than chemical or combined fertilisation. Increasing the fertilisation rate led to higher N and P losses from upland and paddy fields and extended the occurrence time of N and P loss from paddy fields. Overall, this study demonstrates the dynamic processes associated with fertilisation underlying N and P losses from farmland via surface runoff.