Alkalinity and pH are distinctly different from each other, although their definitions and functions can be easily confused. Alkalinity is essentially a measurement of water’s ability to neutralize acids. It’s a measure of the buffering capacity of a system while pH is basically the measurement of the concentration of hydrogen ions in water, in terms of acidity or alkalinity. The alkalinity of water regarding pH issues merely refers to the basic end of a pH scale (alkaline) in contrast to the acidic end of the scale and does not reflect the buffering capacity of a system. It’s easy to believe that water with alkaline pH is likely to be high in alkalinity (buffering capacity). However, this is not necessarily true. Water with a high pH, but a low alkalinity is regarded as unstable. Such water will quickly decline in pH with the natural accumulation of organic acids in aquarium systems.

Ammonia is one of the most studied chemicals in aquaria, and the details of its uptake, excretion and mechanisms of toxicity continue to occupy many research scientists. Because of its high toxicity, it is critically important in both freshwater and marine systems. In fact, it’s one of the few important chemical issues that marine and freshwater aquaria share. Nevertheless, misunderstandings are common about ammonia’s sources, nature and toxicity.



Calcium is one of the most talked about ions in reef tanks. It is critical for the formation of a variety of structures, including the skeletons and shells of many corals and other organisms. Calcium is abundant in various supplements, biological structures, rock and sand, it affects other ions like phosphate, and also how organisms consume and deposit calcium.



Copper is used to treat many parasitic infections in fresh and saltwater fish. To be effective, the copper concentration in the aquarium must be maintained at the therapeutic level for several weeks. Frequent testing is required to monitor the copper level in the aquarium. Some fish species are very sensitive to copper treatments. Copper should not be used or be evident in aquariums with invertebrates, including snails, shrimp, crayfish and corals, as well as in freshwater aquariums or ponds with plants. Tap water may contain copper leached from pipes and, ultimately, it can accumulate in the aquarium.


In the hobbyist sector of reef-keeping, iodine has been found to benefit soft corals, assist in calcification in stony corals and enable crustaceans to molt properly. Iodine can also be used as a dip since it has antiseptic qualities as well.




Magnesium’s primary importance is its interaction with the calcium and alkalinity balance in reef aquaria. Seawater and reef aquarium water are always supersaturated with calcium carbonate. That is, the solution’s calcium and carbonate levels exceed the amount that the water can hold at equilibrium. How can that be? Magnesium is a big part of the answer. Whenever calcium carbonate begins to precipitate, magnesium binds to the growing surface of the calcium carbonate crystals. The magnesium effectively clogs the crystals’ surface so that they no longer look like calcium carbonate, making them unable to attract more calcium and carbonate, so the precipitation stops. Without the magnesium, the abiotic (non-biological) precipitation of calcium carbonate would likely increase enough to prohibit the maintenance of calcium and alkalinity at natural levels.

Molybdenum (pronounced muhlib-duh-nuh-m) plays a vital role in the biology of many marine invertebrates, filter bacteria and seaweed. Among other functions, it is an essential component of certain enzymes produced by the above-mentioned organisms. Regular dosing of this element is vital for the long-term health of the reef aquarium ecosystem. Molybdenum is one of the elements constantly extracted from seawater and should therefore be added regularly.



What to do if you have high nitrates? First and foremost, understanding what nitrates are, their sources, alleviation and relative placement in the grand scheme of overall water quality is absolutely necessary for aquarists. In reality, nitrates by themselves are not that detrimental. What accumulating nitrogenous wastes in the form of nitrate compounds indicates may be symptomatic however, and signal a need to react (slowly) in changing ones management/maintenance of captive marine systems.



Nitrite is part of the nitrogen cycle that takes place in aquariums, and is one of the first encounters that many aquarists have with their aquarium chemistry. The marine aquarium hobby has no shortage of commentary about nitrite, some of which is unfortunately incorrect or misleading. Its toxicity in marine systems is much lower in marine systems than in freshwater systems. Nevertheless, many aquarists erroneously extrapolate this toxicity to reef aquariums and assume that any measurable amount of nitrite is a concern.



The phosphorus atom is one of living matter’s basic building blocks. It is present in every living creature and in every reef aquarium’s water. Unfortunately, it’s often present in excess in reef aquaria, and that excess has the potential to cause at least two substantial problems for reef-keepers. The first is that phosphate is often a limiting nutrient for algae growth, so when elevated it can permit excessive growth of undesirable algae. The second is that it can directly inhibit calcification by corals and coralline algae. Because most reefkeepers don’t want either of these things to happen, they strive to keep phosphorus levels under control. Fortunately, there are several effective ways to keep phosphorus concentration at acceptable levels.


In natural seawater, potassium is a non-conservative major element with a concentration slightly lower than that of calcium. It is a component of aragonite and regular dosing has been implicated in improving the blue coloration of numerous varieties of small-polyp stony corals; the benefits of potassium supplementation are potentially two-fold, then: provision of an element that is 1.) incorporated into the skeletal material of corals and other reef-building organisms for purposes of growth, and 2.) incorporated into pigments that enhance blue coloration of small-polyp stony corals. The importance of potassium to marine organisms is most apparent when beginning to dose it in aquaria with depleted potassium concentrations and/or in which the sea salt mixture used is potassium-deficient; in such cases, changes in the appearance of many corals may be observed within the first weeks of regular dosing.

Silica raises two issues. If diatoms are a problem in an established reef aquarium, they may indicate a substantial source of soluble silica, especially tap water. In that case, purifying the tap water will likely solve the problem. If diatoms are not a problem, aquarists should consider dosing soluble silica. Why dose silica? Largely because creatures in our aquaria use it and the concentrations in many aquaria are below natural levels. Consequently the sponges, mollusks, and diatoms living in these aquaria may not be getting enough silica to thrive.



Scientific evidence indicates that some organisms need strontium. Certain gastropods, cephalopods, and radiolaria, for example, require strontium. Finally, anecdotal evidence from a number of advanced aquarists suggests that strontium levels substantially below natural levels is detrimental to the growth of corals that many aquarists maintain.