Water from closed loop system drains black

I have three floors in my house, all with base board heaters. Each loop is a zone. They all come off my Burnham oil furnace.
I had to drain the system to replace a section of pipe on one of the zones. When the water drains out it comes out really dirty. I know my water is a little hard so is this normal or do I need to add something to the water in the loops when I fill it back up?
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It is normal. That water has been in there for a long time along with any internal residue from the tubing, boiler, etc. .
Oh, you don't have a furnace, you have a boiler. Furnaces heat air. Boilers heat water.
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Water in a hot water heating system always looks cruddy. When you first put water into the system and heat it the oxygen in the water and air will corrode a small amount of metal in the system until the oxygen is used up, and then the water/oxygen will stabilize. When you drain the system or part of the system you allow fresh air and water containing more unstabilized oxygen which will again corrode a small amount of the metal in the system until it stabilized. It is not good to drain the water except where needed for repairs as you will never achieve clean looking water in the hot water heating system.

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