The older Yanmar seawater cooled (raw water) pumps were not very
efficient and could not maintain water flow in a warm engine if any
air bubbles entered the pump. After replacing the cam in the water
pump every 500 hours and the impeller every 100 hours at 6000 hours I
solved the problem by installing an air bleed tube ahead of the pump.
If water is present in the exhaust when running at the dock and it
stops after a while when running under power, then it is a good sign
that the combination of heat and exhaust pressure from the water lift
muffler are preventing the pump from passing small amounts of air.
These are a few of the things done in the ten years I tried to solve
the problem; Moved through hull lower in the keel. lowered the water
strainer below the water line, installed a forward facing scoop on the
through hull, Removed the cylinder head and dissembled the exhaust
heat exchanger, and installed a early warming horn set to sound at 145
degrees exit water temperature.

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