Kind of late in the season:
Remove filter cartridge and dispose of in approved HAZ-MAT manner (Double bag) obtain new cartridge .
Fill fresh tank with a water bleach mix. 1/4 cup to 15 gallons (Need not be precise) and let sit for a at least a few mintues, Close any open low point drains and turn on pump, pump mix through all lines, Toilet, Outside shower, Inside shower, hot and cold
If water heater is bypassed operate valves to USE position replace drain plug if needed, and let it fill with this mix.. let sit at least a few mintues to an hour, I like longer bleach times.
Drain system, remove drain plug on water heater
(NOTE: You can pull the plug before you start and screw in a length of half inch pipe or a hose adapter and extend the drain out past the siding, I like this, then cap the pipe or pinch the hose during filling.
as I said drain, completly.
Fill with fresh water and 1/2 to 1 cup baking soda (Dislove it in as much water as possible first) and again run this through all the lines, flush and so on....
Let sit a few minutes or just let it continue to run.
NOTE: you can dump all this fresh and treated water on ground in most places.. Water your lawn with it if you like.
Finally drain and fill with fresh water.
Run that through all lines. TASTE to insure you have cleared the lines (just a few drops at first)
Drain one last time and re-fill for use.
ATWOOD WATER HEATERS
IF the red wire was removed from the ECO.. Re-connect.
Home is where I park it!