Re: Water in the Motor......Ugh!!
Inline Six Merc's are not manufactured with a cylinder head. The cover over the back of the block is just that, a cover.
The most likely sources for the water intrusion are bad crankshaft seals in the lower bearing cap, and leaking exhaust manifold gaskets. The motor's getting old enough to where either case is possible. Gaskets dry up and become brittle; rubber crank seals deteriorate and de-laminate from their metal shell and leak.
Either problem will require you to pull the powerhead to fix.
A freshwater motor will come apart easily; a Salty Dog is gonna require lots of heat and PB Blaster. Take care not to break bolts. Drilling out stainless bolts broken off in aluminum block is not fun!!!
With the manifold cover off, carefully inspect for signs of leakage. There's also an inner water jacket around the exhaust port, which is prone to leak. Check the exhaust baffle plate for perforations and replace if it's bad.
The lower bearing cap can be removed without splitting the crankcase. Use a puller in the threaded holes in the cap. If you don't use a puller and pry on the cap instead (not recommended), just be extremely careful. The mounting 'ears' on the bearing cap can be broken if you reef too hard. Loosen the bottom (2) bolts which secure the 2 halves of the crankcase together, this may make cap removal a bit easier.
Note how the seals are oriented in the cap, then drive them out; the new ones are pressed into the cap same as the old. I use a thin coating of Permatex #3 aviation dressing on the O.D. of the seals and that's always worked for me. Use a new O-ring on the bearing cap and spread a thin layer of marine-grade grease on the O-ring. Draw the cap back down into the block evenly or you'll bust something! Note that the mounting tabs on the cap are offset and the cap will only fit one way.
The exhaust manifold bolts require 150 inch-lbs of torque, too little and the covers won't seal.
Anyway, that's a quick-n-dirty synopsis of what you'll need to do; plenty of the 'fine' details are omitted; recommend you purchase a manual so you'll have all the info you need to git 'er dun.
HTH & G'luck.........ed