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If you have a vector polygon representing a wetland, then in Whitebox GAT, you just need to convert that polygon to a raster using the Vector Polygons to Raster tool. Use the DEM as the 'Base Raster File' to ensure that output polygon raster has the same dimensions as the DEM. Then you simply need to input this image as the 'Input Pour Point' file to the ...


If you have SAGA installed, try to use Fill Sinks as an alternative, and see if this tool can solve your problem. The tool can be accessed from Processing Toolbox -> SAGA -> Terrain Analysis -> Hydrology -> Fill Sinks.


See section 3.1.5 (p.58-60) in Terrain Analysis: Principles and Applications (Wilson and Gallant, 2000). Figure 3.6 is especially helpful.

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