Water may pass through fine filters, so most systems have a separate water trap in which water can settle out of the fuel and be drained off periodically.
Fuel passes through the internal passages of a simple labyrinth which allows water and debris to settle out. This is then drained off by opening the small tap in the bottom. Catch and examine the liquid for signs of water or contamination. If there are more than a few drops of water, a jelly of water/oil or a small amount of debris, inspect the tank and if possible clean it out. The water trap does not need maintenance, but the cylindrical container can be taken out and cleaned if it is badly contaminated.
Most water separating filters consist of a disposable element filter, fitted above a clear plastic cup as a water trap, so that you can see if there is any water or dirt in the bottom. Give this a routine glance, and drain out any dirt/water if necessary. If this needs to be done often, then it indicates that the tank needs cleaning.
Some prefilters have a water sensor fitted which, when connected to an alarm, provides a visual and audible warning that water is present. This simple device will save considerable engine damage if water has inadvertently entered the fuel tank.
If the water trap is fitted with a filter element (as most are), you must change this at least as often as you change the fine filter. The pre-filter, as it is first in line, is more likely to clog than the fine filter.