Ammonia is the natural waste product of fish metabolism and will accumulate in the aquarium to toxic levels, killing the fish. Fortunately, beneficial bacteria in the biofilter will break down the toxic ammonia. However, there are two forms of ammonia that occur in aquariums: un-ionized ammonia (NH3), which is the toxic form, and ionized ammonium (NH4+), which is essentially non-toxic.
Without going into a long scientific explanation about how and why electrons are attracted to and repelled by atoms, just accept that if a nitrogen atom has three hydrogen atoms attached it is bad, and if it has four hydrogen atoms attached, it is good. The pH (power of Hydrogen) level in your tank determines how many of the ammonia molecules are toxic or non-toxic.
If your tank water pH is at 8.3, most of the ammonia molecules (90 percent) will be in the toxic (NH3) form. But, if the water pH is 7.5, with the same amount of ammonia in the tank, it will be mostly (98 percent) in the non-toxic ammonium (NH4+) form. So, pH (and temperature) affect the form of the ammonia in the aquarium and therefore its toxicity to the fish. The higher the pH and temperature, the more toxic ammonia becomes as more of it is in the toxic ammonia (NH3) form rather than ammonium (NH4+).
Reducing Ammonia Levels
Water changes are important in maintaining the proper water quality in an aquarium. They will help lower the ammonia, nitrite, nitrate, and phosphate levels in the aquarium water and keep the fish healthy. Some people make the mistake of performing a partial water change in a marine aquarium to reduce ammonia levels during the cycling process. Normally, when ammonia levels go up, the pH drops at the same time. By performing a partial water change, the total ammonia levels may drop slightly, but the pH will also rise (the buffering effect of new saltwater), increasing the toxicity of the remaining ammonia. A safer method to reduce the ammonia levels would be to use an ammonia neutralizing product such as Amquel, then perform a water change to "freshen" the water. The ammonia neutralizing products bind ammonia into a non-toxic form until they are broken down by the bacteria in the biofilter, or removed through water changes.
Over time, waste products such as ammonia from the fish will lower the pH (acidity) the water in an aquarium. The more sensitive animals in your tank may not tolerate a pH shift of more than 0.5 units per day, but most fish can handle a 0.5 shift in a couple of hours without any problems.
Use a pH meter or test kit to measure the pH in your aquarium on a regular basis to be sure it is stable and at the correct level for your marine fish and invertebrates. Add appropriate aquarium products to raise or lower the pH as needed. When adjusting your pH level, it is important to do it slowly. If the pH is changed too rapidly, your tank critters can suffer from "pH shock," which can be fatal.