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Ditch‐pond systems (DPSs) play a key role in hydrologic regulation and pollutant removal in agricultural regions, yet there is a lack of quantitative tools that describe their complex transport and removal processes across spatial scales. To fill this gap, a new modeling framework is proposed by implementing three improvements based on the typical watershed models: (a) the explicit rasterization of natural‐artificial drainage, (b) accurate spatial representations of ditches and ponds, and (c) the development of a pollutant‐removal module. This framework is exemplified for a DPS‐dominated catchment in the Three Gorges Reservoir Region, China. The results revealed that 55.36% of the drainage areas in this catchment were dominated by ditch networks, highlighting the significant impacts of artificial factors. The results simulated by the new framework also indicated the great impacts of specific pond distributions on pollutant removal. In this context, pollutant exports in DPSs were distinctly lower than that in natural situation modeling, about 25.14%–46.65% of pollutants are removed by DPSs. On this basis, the scenario analysis also explored the critical placements of ponds and ditches to optimize pollutant removal and to enhance agricultural management in DPSs. This new framework is available for other real DPS‐dominated catchments with potential applications in typical model augmentations and improvements.

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