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Common problems include:

 Inadequate size for the organic load: The filtration should be designed to handle the highest organic load that might be found in the system.

 Inappropriate positioning: Most mechanical filters should be positioned between the system and dedicated biological filters, heat exchangers, and disinfection. Some form of mechanical filtration should be found upstream of water pumps.

 Biofouling/clogging: There should be constant, even flow through filter media. Signs of increased pressure, obvious channeling of water, or bypassing of the filter media should be investigated.

Problems with mechanical filtration often reduce water flow and/or allow the buildup of nitrogenous wastes. Short‐term solutions to problems with mechanical filtration include: back‐washing filters; changing some of the filter media; siphoning animal waste, uneaten food, and detritus; increasing water changes; and temporarily reducing feeding.