Generators on building sites often have some water in the fuel tank, and it doesn't make much difference.
The water sinks to the bottom of the tank. Normally, the tank outlet will be situated slightly above the bottom of the tank. This is to prevent any sludge on the tank bottom getting into the outlet pipe.
As long as the water is below the level of the outlet, you should be OK. But when refilling the tank, the water may be disturbed, and if the system is running, you could then get water in the outlet pipe. Having the system off during and for a while after refilling will allow the water to sink back to the bottom.
To be sure, draining is the answer, and though after this you'll probably still have a a few drops water in the bottom, it shouldn't give you any trouble.