When I once had a flight in a little Cessna, the pilot explained his pre-flight checks. He approached each wing and held a measuring cylinder under a drain c*ck at the lowest point and let out a bit of the liquid. He checked whether there was a meniscus part the way up the liquid (change from water to petrol) and dipped a bit of paper into the liquid; having thrown the liquid on the grass, he lit the paper to prove that it was soaked in petrol, not water.
Most fuel tanks have the outlet slightly above the very bottom so there is space for any contaminating water to sink to the bottom and yet not get drawn into the fuel line. On a boat, the worst that can happen if you draw water into the engine is that the boat will stop - albeit maybe in the path of an oncoming vessel - but you don't want the engine of an aircraft to start trying to run on water when it's in mid-air...