Re: water in the lower unit on 25 hp johnson
Seal leak(s). There are three locations plus the drain/fill plugs: shift rod, drive shaft and prop shaft. If you want to find which is the leaker, pressure/vac test the LU. Drain oil, the pressurize (10 psig is probably OK, but check the shop manual. Put the LU under water and look for bubbles. Rotate/move all shafts, to verify all are OK. A good LU will hold some pressure/vacuum for 30 to 45 minutes.
On a small motor like yours, another approach would be to just replace all the seals.