Unless you've drained some fuel into a clear container and actually seen water, I'd suspect that moisture is causing arcing somewhere between the spark coils and the plugs, or at the plugs themselves. Sometimes this can be caused by dirt accumulated on the outside of the plugs, but it could also be from cracks in the plug wires or boots.
If the problem were caused by water in the fuel, water will get into the carburetor float bowls before you notice a non-start, and it's not going to go away by draining and refilling the tank.
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