My gas hotwater heater when I first turn on the hot water dirty water comes out for a few seconds. The city put in new water lines nearby a few mounts ago and told me to run my water for a while to get dirt out of system. I think I need to clean out the heater of the dirt but how do I do this?

Nothing fancy, you just need to open the drain valve on the hot water heater until the water is clear.

Bad things can happen if the valve hasn't been used in a while. It might be stuck. It might be difficult to open and close and the debris may sometimes destroy the valve seal. This rarely happens. I always replace the standard valve with one with a larger port and always put a cap on it so the quarter turn valve won't accently open because it's in close quarters.