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Common problems with biological filters include:

 Sudden reductions in nutrient availability: Biological filters require oxygen, carbonates, phosphates, and steady amounts of ammonia and nitrite. Changes in these can have major effects on nitrification.

 Changes in environmental conditions: Recent changes in environmental parameters such as temperature, pH, or salinity (e.g. from a large water change with colder water) can have dramatic impacts on nitrification. A variety of immersion medications also have antibacterial activity that can damage nitrifying bacteria (e.g. formalin, chloroquine, enrofloxacin, copper).

 Inadequate size for the organic load: Size calculations are based on the amount of food protein fed per day. If needed, biofilter manufacturers should be able to help with size estimates.

 Biofouling/clogging/channeling: With any biological filter, signs of increased pressure, obvious channeling of water, or bypassing of the filter media should be investigated. Sand filters and trickle beds are particularly prone to clogging.

In the event of problems with biological filters, short‐term solutions can include: back‐washing filters; changing some of the filter media; siphoning animal waste, uneaten food, and detritus; increasing water changes; and temporarily reducing feeding. Bacterial recovery takes time. Additional biological filtration can be seeded from other suitable systems, but this will not help if there are nutrient limitations.