But because of his problem with unioning, I think he should just try and use terrain water instead, unless the water in his game must act in a specific way?
just make these water parts thinner on the Y axis because it will make no difference if your camera is in the water but it will look the same (minus the lines) above water.
is that by a region3 or have you got a frame that does it by CFrame? or what is it because it should still work.
i have made a similar ocean and it is definitely better to have the surface thin otherwise you wont see the surface of the water because once your camera enters a block it is not visible from the inside.
your part is shrinking when unioned because the parts are the largest they can be on the scale, thus when you union them as a single object, it shrinks to the largest possible size of ONE OBJECT, which is 2048x2048.
Try using terrain water instead.