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Through the process of nitrification, bacteria convert ammonia-nitrogen (NH₃) to nitrite (NO₂⁻) and then to nitrate (NO₃⁻). Ammonia and nitrite are 100 times more toxic to fish than nitrate (Somerville et al. 2014). Plants primarily utilize nitrogen in the form of ammonium (NH₄⁺), NO₃⁻ and amino acids such as L-glycine (Rentsch et al. 2007, Sanchez and Doerge 1999). In a fully functioning aquaponic system, ammonia and nitrite values should be close to zero and nitrate should be below 150mg/L. While fish can tolerate much higher levels, upward to 400 mg/L (Timmons and Ebeling 2013), values exceeding 250 mg/L can have negative impacts on plants (Rackocy et al. 2006). From a management perspective, it is important to know the tolerance range of fish and plant species to optimize growth conditions. At excessive levels, these toxic compounds can damage fish gills and stunt their growth.

Alkalinity is an often-overlooked aspect of water quality but is essential in maintaining a stable system. Alkalinity is a measure of water's ability to buffer, or resist, changes in pH (Wurts and Durborow 1992). The most common forms of alkalinity are carbonates (CO32-) and bicarbonates (HCO3-). These carbonates bind to free H+ ions, a result of nitrification, preventing a drop in pH. Water with low alkalinity and a steady rate of nitrification experience wide swings in pH, which can be detrimental to the health of fish, plants, and bacteria. It is recommended to maintain alkalinity between 60-140 mg/L.

Alkalinity is often confused with water hardness. Hardness is determined by the quantity of positive ions, namely calcium (Ca2+) and magnesium (Mg2+) ions, present in the source water. Water from limestone bedrock has a high hardness (120-180 mg/L), while soft water has a low hardness (0-60 mg/L). Soft water is associated with rainwater or groundwater from volcanic bedrock. Water lacking appropriate hardness needs to receive amendments as Ca2+ and Mg2+ ions, which are essential for both plants and fish.

Alkalinity is not normally tested on a regular basis in aquaponics but is maintained through the addition of bases to raise pH. In addition to those listed above, non-chemical measures to increase alkalinity and pH include addition of finely crushed seashells, coarse limestone grit, and crushed chalk (Somerville et al. 2014). Placed in a mesh bag, they can be added to the sump until pH or alkalinity raises to the appropriate level. The size of your system will dictate how long these amendments will be effective and how often they will need to be replaced. Care must be taken to wash these items thoroughly to prevent contaminates from entering the system.

Cycling refers to the process of establishing the biological filter. This can take between six to eight weeks (Figure 17). Nitrifying bacteria are found naturally in the environment, so the process begins by adding a source of ammonia. This can be accomplished through adding fish, fish food, or water from a well-established system, or a combination of these. One of the most common mistakes when using fish to cycle a system is adding too many fish initially.