Not many codes do this type of simulation with fidelity and th ones that do typically cost north of $24k/year to rent or north of $40k to buy though there maybe be some special purpose codes for less dough (say a panel method for vessel resistance predictions). GP codes tend be quite pricey and there are ones with 6 DOF solid object models for path/motion predictions and even fluid structure interactions with deformable bodies. Though probably too expensive an option to get a grip on bobbing apples.
With the paid up code from SWX you could approximate the open channel with a closed duct with an ideal wall for the waters surface - you could then get some information on the flow (velocity gradients, pressure drop estimate amongst other things, any some idea of the turbulence and/or large eddy formations). Might be useful in managing the flow to be where you want to be and avoiding where you don't want to be. Depends what you are after. If you are trying to predict the onset of "white water" you might want to start a search of literature on waves in open channel flows. It might be easy to hand calc some limits to what you want.