Nitrogen Cycle Products
Ammonia, nitrites, and nitrates are products of the nitrogen cycle. To review, ammonia converts to nitrite which converts to nitrate which becomes nitrogen gas (or is taken up as nutrients by algae or other organisms). In reef tanks, measurable levels of these should be kept as low as possible. However, this says little (or possibly nothing) about the rates of their creation and removal so long as those rates balance out. It doesn't matter how much ammonia your tank is producing so long as it is immediately converted to nitrite and then to nitrate and so on. Low levels of nitrates are acceptable but should be monitored regularly to make sure they stay low. While most fish can tolerate low levels of nitrites, most reef invertebrates wouldn't. If after several months any of these compounds continue to show up in unacceptable concentrations in water tests, you *might* have a problem. However, if everything looks well, is eating and behaving normally, there might not be anything to worry about. You might just be due for a water change.
The above is, of course, a gross over simplification of what's
probably going on. And the truth is that we don't have perfect
knowledge of exactly how the nitrogen cycle manifests in any given
aquarium.
Phosphates
The organic and inorganic phosphates (orthophosphates) that show up in
reef aquariums come mostly from food.They can also come from unfiltered
tap water (one reason why it's important to only use distilled or RO
filtered water). Even though coral, fish, algae and virtually every
organism in a reef tank need phosphate in some form or or another,
excessive phosphate levels can be detrimental to coral health and/or
cause algal blooms.
Controlling phosphates means using only
distilled or RO filtered water and being careful not to over-feed your
tank. Growing macro algae is one great way to keep phosphates under
control. Protein skimming and regular water changes also help.