Bathymetry section generation for river or reservoir with an island

How would one go about generating cross sections for a river/reservoir in which there is an island or two. One island is in the main river channel and one off center of the channel Is it possible to resolve the cross section by subtracting the volume of the island? This would make this cross section's volume less and surely this will affect the hydrodynamics and velocities for the cross section before and after The islands are quite sizeable and almost 5-15% of the volume of water. Any suggestions would be appreciated