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Well that would be the problem...cleaning out the entire filter kills off all the beneficial bacteria that keeps the tank balanced and the fish alive. If you do not have a filter that allows you to partially change the media I suggest investing in something like an aqua clear filter. There is rarely any need to actually clean out a filter that is functioning properly. Regular replacement of carbon (if used) is about all that is neccessary along with an occasional rinse of the the sponge portion of the media (in tank water to avoid killing the bacteria). It is a safe bet that any problems you are having with this tank is in some way related to the cleaning of your filter.
 

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Yes the water should clear out eventually. The cloudy water isn't what is going to hurt your fish, the tank being forced to completely cycle again is what is going to hurt the fish. If the ammonia and nitrite spikes don't do them in, some disease will after it gains a foothold while the fish are stressed from the poor water quality.
 
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