Lisa, It sounds like you have galvanized pipes going to the second floor and it’s rusting thats why you are getting that brown water. I would guess the supply pipes to the first floor have been changed to copper. There are only 2 ways to correct the problem, (1) replace the old galvanized pipes. (2) install a water filter at the faucets on the second floor. I hope this gives you some ideas. Good luck,
Scott