If you are flying east bound through a mass of air that is moving from east to west (opposite direction to your flight path) at 100 kts (pretty big headwind) and your true airspeed is 250 knots (actual speed through the air) your ground speed (speed over the ground) will be 150 knots.
So, without applying any other variables, the time from your departure point to your destination will be based on 150 knots ground speed. If your destination is 150 nautical miles from your departure point, your enroute time would be about 1 hour.
Simple as that. (Ground speed) "GS accounts for the wind" as you say in your question.