If there are large amounts of water, it should settle within a minute of ten-fifteen. If it is clear after that time, there is probably (!! i am not liable for anything here...) not enough to do alot of damage.
Personally, i drain before each flight, fueled or not, rain or not, you never know if the person before you did a proper job, unless you own your own plane, but even then...)
The water can come from different sources.
-water in the fuel
-watercondensation in tanks (overnight, no full tanks, etc...)
-watercondensation in fuel truck
-leaking seals/rain
-IBLB-