Just finished with this issue myself, tried cleaning the intake filter and flushing the system with bleach, that had a great impact on the water flow, but didn't fix the problem.
Also tried running the a/c when the boat was underway as suggested by my mechanic, that's supposed to force the water through the system and clear a clog if you have one, but that didn't work either.
Feel the pump, if it's really hot when the error occurs, then you need a new pump, also listen to hear if it's pumping consistently ultimately, we replaced our pump.
The a/c works like a million bucks (or at least a thousand bucks) now!