I've never done a 4 layer board and am not familiar with the process of manufacture for them. Will the external layers isolate inner layers from water if say, I will be putting the board into water for long periods (months) of time?
No. Ordinary PCB technology does not protect against moisture ingress over the long term - that's actually a very, very difficult problem to solve where joints between different materials exist.
The material most commonly used is FR-4 which is a composite material composed of woven fiberglass cloth with an epoxy resin binder that is flame resistant. Because it's a woven cloth, the water can still go through the edges.