There are two lines to the bottom of the fuel tank. The larger one (thicker) is the fuel line, and that goes to the carb.
The smaller (thinner) line is the vacuum line, and that one goes into the side of your intake manifold.
You need to remove it from the manifold, and suck on it to create a vacuum. This will allow the fuel to flow. I open the bowl drain screw, and catch the fuel in a glass jar. Inspect that after a minute or so. You WILL see a layer of water if it is in there. It will be easy to spot if you tip the jar so the water collects in the corner. (corner of a round jar???) Then leave the drain open, and suck on the vacuum line. Allow an ounce or so of fuel to flow, and inspect that.
If you do find water... SeaFoam works great to absorb it in the fuel system, and it is a great preventative maintenance type product. If you never used it in the bike add 2 ounces for two consecutive tanks of fuel, and then one ounce every fourth tank full. It will prevent problems before they occur.