Hi David,
Hav a look at the INFLOW_MAXDEPTH bc keyword. The basic idea is in the pre-processor you need to specify all possible boundary condition cells that the inflow may enter through the length of the simulation (usually down the length of the drowned river bed). The INFLOW_MAXDEPTH value in your temporal boundary condition file then controls which of the cells are valid bc cells for any timestep, so you can limit the inflow to only come in where the surface meets the river.
Hope this helps.
Chris