(Seemingly like always here...man I do like that) Nothing but gr8 replies!)
Fireman had a legit. concern, however biocide CAN be replaced by gasoline (ideally ethanol free) and it's a lot cheaper than biocide. It Also WORKS BETTER than biocide, in that most of them don't fix the Original Poster's(OP's) problem AFTER the Fact, when You have the BUGS in the system. Gas WILL Kill the bugs.
Polishing is done AFTER You put the gasoline in to the diesel (at a factor of 5%. eg:50 gallon tank, full...pump out 3 gal. of diesel, add 2.5 gallons 87 octane. Leave it alone for a day.
Come back, hit the seperator & get all the water
off the bottom...Your sight glass lets You see the h20; pump out the tank in to jerry cans using a strainer on the outlet side of the pump (beit hand or electric
operated, avoiding sparks...drills MAKE SPARKS) covered with a coffee filter. The crap making it thru Your pump & getting caught in that strainer/filter will be enlightening. This is all ideally done from the INSIDE of the boat, from the BOTTOM of the tank via the pickup line and Aft of Your primary strainer & either aft or forward of Your water seperator.
Once You have ALL the fuel out of the tank, take another coffee filter & put it over the outlet nozzle on the jerry jug, securing tightly with twist ties(don't use zip/wire ties here unless You have the "removable" type), and begin refilling the tank with the jerry jug(s) stopping often to check the filter to make sure it's not clogged; when it is, carefully remove, replace & continue filling. It's a long, drawn out process, however it also costs about the price
of a pack of coffee machine filters, for in a pinch if You didn't have enough jerry jugs, Your friends who own diesels...probably do & wouldn't mind loaning them to You for a "day".
There's no need to discard "bad" diesel, as it isn't. We used this trick, plus mixing in some (less than 15% based on the room in the tank) fresh fuel AND "Cetane" Booster on 8.5 year old fuel on a boat that had been on the hard
(even though I thought the best shot simply taking it home to add to the parts washer..& I was wrong...afterward that perkins
burned every ounce w/o the first hiccup)
Once You've completed the entire process, reconnect the supply line AFTER you Change any/ALL racor/other in-line filters & buy 2 of each while at the store. After the tank is exhausted, or been refilled from half down ideally at least twice, go in and swap those filters again. Problem solved
...most likely, for ever. Getting the trash out of the tank (including dead algae) was the goal...recycling the fuel back to a serviceable safe & reliable condition was the benefit.
Use these tactics (minus the gasoline...we use lye instead to seperate gylcerin) for making biodiesel, & the straining process (to clean Straight WVO) is exactly the same. Settling of particulates we look forward to on the environmentally friendly "oil" side of this, however on sail/power boats, YOU don't...for that "trash" will get stirred up again soon as the boat gets back to the old "roll, pitch
& yaw". DEAD ALGAE will BE "Particulates". Washing
the tank is easy w/just a few gal. remaining if You have access directly above...not so easy if deck
fill is via the rail; either way filling half way again, down the road & repeating the process in a few months cuts filter replacement costs to nil.
It's almost impossible to have "dead" diesel. Cleaning(/"Polishing") is is far more practical than the costs for disposal, both environmentally & financially.
Our "keeper" boat is set up with 2 sight bowl/water seperators in a row, & 2 racors behind that before the fuel pump
. Never had a problem.
Military skid mounted diesel gennie has THREE Racors/Paper filters stacked in a row...point is an "extra" in-line filter (shy of it being clogged, which vs. injector pump
is a GOOD Thing) never hurt & has saved many of us much grief. If You don't have it, consider adding it.