Short answer
Draw from the lowest point of the tank — a drain, sump or dip tube — into a clear container and remove fluid until only clean fuel comes out. Then find the entry path, usually a deck fill seal, a breather or condensation. Heavy contamination needs professional fuel polishing or a tank clean.
You will need: Clear containers, hand pump or dip tube, absorbent pads, torch
Water sits below diesel, so it collects at the lowest point of the tank and stays there until the boat moves enough to stir it up. That is why filters block in rough weather.
Removing it
- Work from the lowest point — a drain valve, sump or a dip tube run to the tank floor.
- Draw into a clear container so you can see the interface between water, sludge and fuel.
- Keep going until what comes out is clean fuel, not a lightening emulsion.
- Capture everything. Diesel and oily water are pollutants and must go to an approved facility.
Then find how it got in
Removing water without closing the entry path just schedules the next removal. The usual sources are a leaking deck fill seal, a breather taking spray, condensation in a tank habitually left part full, or contaminated fuel taken aboard.
When it is beyond a drain
If the tank holds sludge, microbial growth or rust scale, draining water off the bottom will not fix repeat filter blockages — the solids are the problem. That calls for fuel polishing or a proper tank clean, and on a badly corroded tank, replacement. See why a fuel filter keeps blocking.
Keeping it out
Keep tanks full to limit condensation, particularly through an Australian wet season or a southern winter lay-up. Drain the water separator on a schedule rather than when there is a problem. Treat with biocide only as directed, and only after the water is gone — killing growth in a wet tank leaves the dead matter behind to block filters.