You really should look into the nitrogen cycle of aquariums.
1. All water from the tap needs to be conditioned BEFORE you put it into your aquarium, or it will harm your fish.
2. If you clean your biological filter, you will harm the bacteria which turns Ammonia into Nitrites and Nitrites into Nitrates which seems to be a problem already. Mechanical filters can be rinsed in used aquarium water.
Do you have high Nitrite or Nitrate?
You may want to read this article on tank cycling --
http://www.algone.com/cycle.htm This information is very useful and could help you out. Good Luck!
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