In my experience (bought boat in 2015 with 2 - 79 gallon diesel tanks containing about 120 gallons of diesel unknown fuel age), there is not always a lot of water. But even a little gives a space for the critters to exist. They grow breed, poop and die in the interface between water and diesel.
I addressed them by adding fuel, adding additives to kill and resolve them, filter replacements
(at one time after every 25 hours, I was sucking off the bottom of one tank while driving the boat through 3 ft chop), and polishing fuel by transferring fuel from one tank to the other. I now have one tank 95% clean and one to go.
My plan was to use the fuel and the boat while I worked the problem. The costs of a preemptive strike, that would have been installing cleaning ports in both tanks, power scrubbing both tanks, and polishing the fuel was estimated at $2,500. I thought $20.8 a gallon for the fuel was a bit steep.
I've spent about $2.40 a gallon on filters,
a new Racor 500 filter unit
(I needed to replace the original Ford truck filter anyway,
but I threw it in to the cost estimate at $210) and chemicals.
We each have to choose our path to better boat experiences.