Many people dont use canister filters on saltwater tanks because they have this effect. Mechanical filteration traps waste and allows it to break down within the system creating ammonia > nitrite > nitrate. Where as protien skimming removes the waste before it breaks down. If you want to keep your nitrite and nitrate down you will need to clean out the canister frequently or remove the media from it that is trapping and holding waste. Or discard the canister completely and just get a new or larger protien skimmer.
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