Most of the boats at WDW do not have any trouble with water levels for
ECVs. The only ones that I have heard can be a problem are at Wilderness Lodge and Ft. Wilderness.
The large Ferry Boat between the parking lot and Magic Kingdom never has a problem with water levels.
The friendship boats on the Epcot/MGM run never have a problem with water levels
The Sassagoula Ferries never have a problem with water levels.
The smaller launches between MK and Polynesian, and Grand Floridian are not accessible, but there is always the monorail.
The smaller launch between Ft. Wilderness, Contemporary, and Wilderness Lodge is not accessible, but there is a larger boat between Ft. Wilderness, Wilderness Lodge, and Magic Kingdom that is accessible. That is the only boat that sometimes has water level problems. Also, that may have mostly gone away, because they have discontinued the bus that runs from Ft. Wilderness to Wilderness Lodge to TTC.
There is a bus that goes from Wilderness Lodge directly to Magic Kingdom.
If you need to get from Ft. Wilderness to Magic Kingdom and the water levels won't accomodate you, then ask at Guest Services for a ride, or take the path from Ft. Wilderness to Wilderness Lodge and take the direct bus to Magic Kingdom.
I hope this helped.
Carol