Turn off all the burners and give the cooktop at least a half hour to completely cool down. You don't want to try cleaning it if it is still hot.
Dampen some paper towels and apply a small amount of cooktop cleaning cream to them. Cooktop cleaning cream contains isopropyl alcohol, which is what is often used for cleaning lenses and other types of sensitive glass.
Wipe down the water marks with the paper towels and cleaning cream until they vanish. Apply pressure as needed. Let the cleaning cream soak on the water marks for a few minutes if they are particularly stubborn, then try wiping them off again.
Buff and dry the area with a non-abrasive cloth. The cloth must be very soft to avoid scratching the glass. Repeat the process as needed.