They call it a sight glass for a reason. Water is heavier than fuel, so check the filter for a clearer liquid, or debris at the bottom. If you see something suspicious, close the fuel cutoff, remove the filter and clean out the housing.
I think it's a good idea to look at it before each time. It only takes a second to check things out. Do it as you're checking the old, coolant, etc.
A lot of the water separators have a red ring that will float on top of any water. So if the red ring is sitting on the bottom of the bowl you are good. If the ring is above the bottom simply drain until ring sinks to the bottom.