No question, you should try to avoid fueling while the tanks are being filled, but water and small particulate settle fairly quickly in gasoline. 1 hour after fueling, everything should be fine.
Jet fuel (aviation kerosene) and other middle distillates like diesel take longer. The standard is to allow 1 hour per foot of tank diameter. So most aviation tanks are left at least 8-10 hours, depending on size, and most also have floating suctions, just to be sure that nothing gets picked up. Then the fuel is filtered...on it goes in the aviation fuel business...