I was filling up the radiator with coolants the other day and I noticed the water inside was brown so was the actual radiator but when they rebuilt the motor I put in a new radiator what could this be?
Did you only use water or did you put in antifreeze/coolant too? The PO of my truck put in a new radiator a couple years ago and only used water. When I got it, the water was very rusty. Antifreeze has chemicals in it to prevent rusting of your coolant system. I drained and flushed it a few times, filled it up with antifreeze/water to the specified amounts, and it has been fine ever since.
I just realized that you are from Canada, so I am now going to assume you have had antifreeze in there. Just flush the system, refill with water, drive for a day to help clear the whole system, drain and flush again, fill with appropriate amounts of coolant/water, and you should be golden. Maybe repeat the process again in six months.
Use the concentrate type & distilled & filtered water! The type or color of the coolant is only important if a aluminum radiator.