You will need a supplemental permit. Actually, a licensed contractor will need the permit, because water heaters and furnaces are not DIY in DC.
You can get supplemental permits without a building permit. Happens all the time for things like installation of gas stoves or water heaters. DCRA’s website has pretty good information. You can see that you don’t need a permit for certain replacements, such as doors and gutters, but water heaters aren’t among them.