How to Clean Boat AC Seawater System

Seawater Flow Issues in Boat Air Conditioning

If your marine air conditioner isn't working properly, one of the most common problems is restricted flow of seawater through your ac unit. If your seawater pump seems to be struggling or if you're getting HPF or High Pressure warnings, you likely have some barnacles or other debris in your seawater cooling system.

Before doing any sophisticated or more involved work on your marine circulation pump or your boat's air conditioning system, remove and clean all the filters and do the same with your strainer to maximize heat transfer (MAKE SURE YOU CLOSE YOUR SEA COCK FIRST).

Groco Strainer Cleaning. Magnetic Drive Pumps. Marine AC Pumps.
Probably not a lot of water flowing through this strainer...

Check out our Marine Air Conditioner Troubleshooting page for these and other recommendations on determining why your boat ac isn't working properly. Whenever working on your sea water pump, make sure that you've closed all the valves below sea level.

Once you get through those, if your thru-hull discharge still seems to be discharging less water than previously or isn't flowing smoothly, your marine heat pump or marine air condition system won't be able to pull heat or dump hot water into seawater quickly enough for optimal performance.

We see more water flow issues on boats that are moved less often, boats that are stored in well-protected marinas or harbors, boats that often travel in shallower, muddier water and boats with older marine ac systems. Most water flow issues stem from obstructions in the cooling water system - usually mud, algae and/or debris.

To clean it, you'll need to put back pressure on the system in a way that doesn't damage your heat exchanger or other marine pumping equipment. We recommend using compressed air to do this. Most seawater cooling troubleshooting ends up being about removing barnacles from boat ac systems or debris in the salt pump itself (magnetic drive pumps or centrifugal pumps are most common).

Cleaning out the hoses on a boat ac unit
We can flush debris out of your boat ac system.

Here are some examples of error codes that can be caused by insufficient saltwater flow and/or high water pressure in your marine air conditioner.

Marinaire: error code E4 or error code E7

Webasto Marine: error code A01, error code A02, error code A15, error code A20, error code A23, error code A28

Mermaid Marine: error code P-6, error code P-9

Dometic Marine: Hi-PS, HPF (High Pressure Fault), Lo-Ps, HPS

Determining the Water Flow Rate in Marine AC

To check water flow, you can use "the bucket test"

Thanks to Marinaire for providing the tables below for calculations. Low salt water pump flow is a common issue and will result in an E4 code on Marinaire units. In order to test whether your boat's ac pump is circulating enough water, you can use the following "bucket test":

  1. Turn on your circulation pump (i.e. March Pump) - may require turning on AC unit - and open your seacock
  2. Grab a 5 gallon bucket with a line attached to it. NOTE: most 5 gallon buckets are actually more than 5 gallons if filled to the rim. Generally they will have a ring inside the bucket that shows the true 5 gallon mark - usually about 2 inches from the top
  3. Grab a stopwatch that measures seconds (iPhone or Android timer, for example)
  4. Begin filling the 5 gallon bucket and start your stopwatch
  5. When the bucket is filled to the 5 gallon mark, stop the stopwatch. Note the time (in seconds) and refer to the table below to determine if your flow rate is sufficient. If you have multiple ac units using the same pump, add the GPH requirement for each and adjust time by the same % (i.e. twice the GPH means the bucket should fill in half the time)


6000 BTU

Must be filled within 120 sec

9000 BTU

Must be filled within 100 sec

11000 BTU

Must be filled within 75 sec

14000 BTU

Must be filled within 65 sec

16000 BTU

Must be filled within 55 sec

20000 BTU

Must be filled within 40 sec

24000 BTU

Must be filled within 35 sec

For current Marinaire models, these are the recommended minimum water flow rates:


300 GPH


300 GPH


500 GPH


500 GPH


500 GPH


1000 GPH


1000 GPH

How to Clean Your Seawater Cooling System

We have built a special tool that we use to clean out seawater circulation systems for our customers. We use compressed air to push a column of water that washes seawater piping from the seacock to the through-hull inlet to the thru-hull overboard discharge.

March Pump
Our setup to clean boat ac water pump lines.

Our tool is made of stainless steel and other marine grade components. We use it to blow compressed air through the water circulation pump, inlets and hoses. Be careful if you try to build this yourself that you use the appropriate fittings and connectors.

The tool we use allows our marine ac technicians to remove all the debris from your circulation pump and related plumbing. We often find that most marine air conditioner pumps collect a lot of debris in a typical boating season - especially when boats are kept in well-protected marinas.

In the video below, you can see how we do this. You'll be able to see how much dirt and debris comes out and how much the flow level improves afterwards.