Hi,
I'm not sure what you mean with the results look wavy. The figure attached is water depth, so this is the thickness of water on top of your river bottom. I would look at free water surface rather, this should be a smooth(er) surface if sub-critical flow.
Having a stage discharge curve means you are doing non steady simulations, I would suggest you start with steady state first, fixed downstream water level with slowly increasing discharge towards the steady state.
Hope this helps,
Patrick