While the waste created by the fish may act as a valuable source of nutrients for the plants, it can also hurt the fish themselves if too much builds up in the system. Both dissolved gases and solids, and more obvious large, solid waste can cause numerous problems if allowed to build up. This includes, but is not limited to:

• Damage to the gills of the fish; leading to inefficient oxygen absorption, slow growth rates and extra risk for disease.
• Higher rates of dissolved ammonia in the water; which can damage both fish and plants.
• Biochemical oxygen demand (BOD); a factor that causes lower oxygen concentration as the waste is used up by the bacteria breaking it down.
• Development of anaerobic and heterophobic bacteria in the biofilters that are harmful to the system rather than helpful.
• Increased clogging of filters, valves, and pipes due to both physical waste accumulation and thicker biofilms of bacteria feeding on it.
• The release of toxic hydrogen sulphide from the anaerobic digestion of layers of waste trapped where dissolved oxygen can’t reach.

Both mechanical and biofilters play an important role in managing waste in both dissolved and solid formats. While mechanical filters are primarily designed to trap solids, they also become hosts to nitrifying bacteria that help convert ammonia to nitrites and then nitrates. The biofilter is home to the majority of these bacterial colonies, but every filter surface still contributes to the total effect.