Good morning,
What you can do is do the initialisation through a user_fortran file with INITIAL CONDITIONS="SPECIAL" in your steering file using the subroutine USER_CONDIN_H to define the water height at the initial state. You need to know exactly the contour of your river area and then define a polygon around this area. And finally, to set the water depth withing the defined polygon, you can use the subroutine INPOLY.
Good luck,
Jean-Paul