You have basically three options for that kind of thing, single/multiple lip seals, prop shaft packing and machined grooves to pull the water out (as the shaft rotates, it will leak when not moving). Those options can be employed individually or together single or multiple on a given shaft. For example a commodity submersible sump pump may have 2-4 seals stacked in series to keep water out of the motor and an engine crankshaft typically uses a lip seal paired with machined grooves. Also I'm probably forgetting something so you probably actually have four options.

A quick google search doesn't make it clear which ones the amphicar uses where.