Older Yanmar pumps have trouble keeping the pressure up to maintain
the flow unless the pump clearances are correct. This is more of a
problem on boats with hot water heaters, engine driven refrigeration
and water-lift exhausts.

When replacing the raw water pump impeller it is important to check
the clearance between the parting surface and the impeller. Make sure
the impeller is all the way in the pump then with a straight edge and
a feeler gauge check the free clearance of .001 to .002 of an inch. If
there are too gaskets on the pump plate instead of the thin one
supplied by Yanmar, pumping pressure will be effected.

On 2GM and 3GM engines that are salt water cooled a stuck closed or
missing thermostat will bypass the water all the time causing the
engine to overheat.

From the author of four books on boat refrigeration.
http://www.kollmann-marine.com