Non-point source pollution (NPS) is difficult to manage for watersheds, due to the scattering of pollution sources and uncertainty over the time it takes to accumulate. Since local agriculture and poultry rearing prevail, NPS occupies a large proportion of local pollution. In this paper, we modified the runoff module of the Soil and Water Assessment Tool (SWAT) to study the distribution properties and the effect of control of NPS in the Binjiang watershed in Southern China. The model was run from 2005 to 2014. The runoff simulation’s accuracy had apparently improved compared to the original model, as the Nash coefficient (Ens) had improved from 0.72 to 0.89, and the determination coefficient (R2
) had improved from 0.75 to 0.91, an improvement in accuracy of 23.61% (Ens) and 21.33% (R2
). Thus, the modified model (SWAT-m) is more adaptable for the simulation of extensive non-urban watersheds in subtropical monsoon climates. The validated model was used in further analysis. The results show that 82–90% of total nitrogen and 83–89% of total phosphorus were concentrated in the period from April to September annually. Through the introduction of the pollution generation potential parameter Φi
, we obtained the descending order of all sub-basins in terms of their pollution generation potential. The critical source areas (CSAs) were found to be the northeast sub-basins in lower terrain that is used mainly for agricultural applications, accounting for 53% of the total watershed. The accumulation time is April to July, occupying 69% of annual generation. The simulation of management measures showed that NPS control has a good effect, with a 15 m filter strip in CSAs. Ammonia nitrogen and total phosphorus can be reduced apparently by 32% and 43%, respectively. The results may provide support for the management of NPS in watersheds under similar conditions.
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