I think you would have to approximate it. Instead of creating a single internal boundary condition along the mesh cells on the bank of a reach, divide the source among cells along the bank. The inflow hydrograph can be scaled. Say, if you use the same hydrograph in 100 cells, scale the inflow by 0.01. There would be 100 boundary conditions, rather than one.
It gets further from what you are trying to do, though. I don’t expect you can have different internal boundary conditions in two adjacent cells, so the source cells would have to be separated by cells that do not have boundary conditions. Also, I expect that the internal boundary condition cells cannot share faces with a lateral structure.
Try it though, I haven’t yet. I am more familiar with external boundary conditions, where I assign a slope of the topography into the mesh, and flow enters the mesh at the lowest part of the section.