In order to help, a little more info is going to be needed. there alot of things that could cuae the problem your haveing. Please answer as many as there you can so the issue at had can be narrowed down.
-Tank Size:
-How long has it been setup:
-How many fish:
-Type of fish:
-Size of fish:
-Filtration:
-Ammonia Reading:
-Nitrite Reading:
-Nitrate Reading:
-PH Reading:
-Temperature:
-Any recent changes in tank decor or tank mates:
-Any medication:
-Food what kind how often:
-When was last water change and how much:
The water being discolor the way it is makes me wonder if you are doing enough on water change. Are you vacuumeing too when you do your wc?