Water level issues are always a possibility, but the water levels there seem to be pretty stable - at least, I've not seen reports of problems.
I think the ends if the docks are also floating, which helps keep the boat and dock more level.
Boat captains also have ways of dealing with the water level by things like loading the ECV first if they need the boat to be higher in the water or loading the other passengers first if they need it to be floating lower.
There are also nice paved walkways between those Epcot area resorts and both Epcot and the Studio. So, even if the boats were not running, you should have no problem.