I built a breakwater from the end of my moat out into the water for about 10-12 floor lengths and then turned 90 degrees (away from the base) and continued it for the same distance.

This seems to have stopped all but the very determined from coming into my base via the water.

If they fall into the moat and then walk to the water and come in just build a single stone (2x1) wall across your moat to stop them.