We always should assume that the tank has some amount of water on the bottom. You made a trip in rough water and it has clouded the fuel during the trip.
Where did I get the water? Check the fill port gasket and vents to see if that is how the water entered the tanks.
Water may have been delivered to you but it is hard to prove without going back to the source and inspecting their supply.
Drain the separator and keep a sample of the fuel. Letting the boat sit for a day or two and restart the engine. Compare what you see in the separator now with the sample you kept. If the problem came from water on the tank bottom, after sitting for two days in calm waters the fuel should clear up.
After assuming water is on the bottom of the tanks we must get it out. Steel Camel, https://www.steelcamel.com/, has a water absorbing sock that will work if you can get it into the tank. Or we must find a way to get a pickup tube to the bottom and suck out the water. No telling of there is 1 gallon of 20 gallons of water on the bottom.
To clean what you have is to install a Dieselcraft Fuel Purifier followed by the Racor and recirculate for as long as it take, 8 hours, and the fuel should clear up.
DO NOT add any additive. Some additive promote “allows the water to be burned off.” Water burns? Engine manufacturers allow ZERO water in the fuel, burnable or not. ZERO water. The only way to remove the water is a mechanical purifier/separator, absorbing media or a vacuum cleaner but not burning.