In flow simulation you can move the fluid around the assembly but not the assembly in the fluid.
So for example you could do an external analysis where the fluid goes by at a certain speed and you could measure the force and torque on an arm to figure out the motor strength needed to hold it in place.
If you can figure out a force function, you could do some of what you want in motion. Extend to simulation if you want stress.
For waves, you'll need to look at another software. Simulation doesn't deal with waves and open surfaces.