I believe there are several treatments such as Biobor that will slow down the formation of the slime that grows on the interface between the water in the bottom of your diesel tank (if any) and the fuel itself.
Once water is present, I don't believe these treatments will dissolve or emulsify the water such as the alcohol-based treatments might do in gasoline.
This is both good and bad. Once you observe a small amount of water in the bottom of your fuel filter - either directly or by sampling the filter and letting it settle in a small, tall, glass container, you can remove the water mechanically as Brian suggests.
I use a small flexible plastic tube such as a refrigerator ice maker supply tube, and tape it to a plastic rod like the kinds the exterminators use to mark a sprayed lawn. Then I remove the tube that draws fuel from the top of the tank, clean and remove the screen and insert the small clean out pipe. I attach the pipe to a sall electric "universal" fuel pump and to a racor filter - leading the output back into the tank.
I pump in a circle until no water shows up in the filter for 30 minutes of pumping. This takes several cycles as I stop and drain whatever water is found frequently until none is observed.
You can pull a cup or so of water out on each cycle. I use a soda bottle to draw off the water by holding it under the valve on the bottom of the Racor, decanting the fuel back into the tank if any gets into the bottle.
There is nothing wrong with the fuel and most of the tank is not really dirty, just water and slime that you can filter out.
Once you are done, assemble and inspect the fuel separator on the bottom of the Racor every few hours until no water is observed - then change the Racor element once more and you should have no more problems.
Dirty and time consuming, but fairly easy and reliable.
