Nikon AF-S 300 f/4 focusing problems

Your camera can be the fault here, mine had some of the AF-points that always told the AF-engine to focus closer no matter what, if I selected those AF-points.

And if I used all of them, they were selected when there was no other contrast to be found for the AF-engine. That more or less rendered the all-focus-point-mode useless.

But a trip to Nikon to get the AF-points calibrated fixed this issue, which is quite common according to Nikon, especially if a camera has been dropped.

The easy test for you to do, is to try another lens, and see if that is the same, you should be able to provoke the issue by AF'ing against something with little contrast. (and you maybe be able to select AF-point 1 by 1 to find the faulty one).

When that is said, focusing over water almost always results in some back-focus, unless careful aiming with the AF-points is performed. Micro-adjustment is not the right way to fix that, it just the way water works on the AF-system.