Ammonia (NH3) is a gas which dissolves in water to form ammonium hydroxide. Being a base, it dissociates into its ions, OH- (hydroxide) and NH4+(ammonium). But a small proportion remains as ammonia and this is what harms fish. Virtually all our test kits measure total ammonia - that's ammonia and ammonium combined. But it is possible to work out how much is in the more toxic ammonia form. This ammonia is usually called free ammonia to distinguish it from ammonium.
The amount in each form varies with temperature and pH. Temperature varies little in tropical tanks so the amount of free ammonia in our tropical tanks is dependent mainly on pH.
The equilibrium constant for the equilibrium between free ammonia and ammonium is well known and there are on-line calculators to determine the amount of free ammonia at any given pH (and temperature). This is the one I use
Aquarium calculator; Estimate the free (un-ionized) ammonia (NH3) concentration, given the total ammonia concentration.
www.hamzasreef.com
For fresh water, salinity is set to zero and the other parameters entered, and free ammonia is given in "NH3 concentration".
Fish can cope with a free ammonia level of 0.05 ppm for a couple of days; and up to 0.02 ppm for several days. For long term fish health, free ammonia should be well below 0.02 ppm.
@seangee wonders what happens at very low pH where there is virtually no free ammonia. At pH 6.0, even a total ammonia of 8.0 has only 0.0046 ppm free ammonia. But years ago I was taught that ammonium is not non-toxic, just less toxic than free ammonia. This is not mentioned nowadays, and I know of no study to show the effects of high levels of ammonium on fish. If any member does know of such a study, please let us know.
We know that at very low pH, the 'ammonia eating' bacteria do not grow in our tanks but that there is virtually no free ammonia. We also know that at high ammonia levels, a different species of 'ammonia eater' grows which is one reason we need to make sure we do not add too much ammonia for fish cycling.
Question - are the bacteria which grow at high total ammonia levels inhibited by low pH? Or will these 'high ammonia bacteria' grow in our tanks even when pH is very low and keep the ammonium level at a certain point?