Water in Diesel Question

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As said remove the water any way possible asap. Put in the “heavy” dose of your favorite biocide. Then let the boat sit for awhile. Bugs grow at the interface between the water and fuel. Even though with the first draining you think you’ve gotten out the water it’s likely you haven’t. Unless you’ve drained very slowly the contains of the tank have been agitated so it likely there’s some water left. Worthwhile to drain that hopefully small amount off with a second drain. If you’re not running through racors you’re done if so polishing is in your future.
For our current boat the main engine draws from port tank and genset from starboard. Even though there’s a large cross over the port tank had water and growth shutting down the genset when we first bought her. Fortunately she’s appropriately vavled. Was told to do the above. It worked beautifully and we didn’t need to polish. Apparently killing the growth first and draining twice to allow separation in between is the key. You also want to draw off a bunch of what you think is clean fuel with each draining so make sure you can dispose it and the water appropriately. Yard may charge you a disposable fee.
P.S. if you can use weight to tilt the tanks so they’re lower where you are draining. You’ll leave less water in the tank that way.
A word of caution on bio-cides. I bought a boat several years ago in which the PO thought "more is better" when it came to bio-cide, it is not. The (gross amount) of excess bio-cide that accumulated over time formed a crystalline structure in the fuel system. I had to remove the tank for cleaning as well as replace all the fuel lines, valves etc. I understand your intention is to temporarily dose the fuel, but be careful about how much is routinely added.
 
A word of caution on bio-cides. I bought a boat several years ago in which the PO thought "more is better" when it came to bio-cide, it is not. The (gross amount) of excess bio-cide that accumulated over time formed a crystalline structure in the fuel system. I had to remove the tank for cleaning as well as replace all the fuel lines, valves etc. I understand your intention is to temporarily dose the fuel, but be careful about how much is routinely added.

Sometimes it is necessary the shock treatment. Guessing; 1/2 tank fuel. Add enough biocide for full tanks, take the boat to stir up the fuel the use the fuel polisher, fill up the tank, polish again.
 
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