I need to correct the TanDEM-X data on the water surface, because the values are negative and it is impossible to calculate morphometric indices for mapping and relief analysis.
Try using the FlattenLakes tool available in the Whitebox. If your water body polygons are lakes, this will be a very useful tool. https://www.whiteboxgeo.com/manual/wbt_book/available_tools/hydrological_analysis.html#FlattenLakes