There are two forms of ammonia that are present in your aquarium with any positive ammonia test reading. These two forms are Free Ammonia NH3, which is very toxic to your fish, and Ammonium NH4 which is non-toxic. The sum of these two forms (NH3 + NH4) represent your aquarium’s Total Ammonia Nitrogen, abbreviated as TAN.
When people talk about “ammonia readings” on a forum or elsewhere, they are almost always referring to a TAN reading. All of the most popular tests, including the API Master Freshwater Test Kit, API Strips, and Tetra Strips are testing for TAN, meaning they are providing the sum total of both the toxic ammonia and non-toxic ammonia forms. So if you get a reading of 1.0 ppm Ammonia, that is 1.0 ppm TAN and some of that is Free Ammonia NH3 and the rest of it is Ammonium NH4. This means that only a portion of your overall ammonia reading is toxic to your fish.
The amount of toxic Free Ammonia NH3 is determined entirely by your aquarium’s pH and temperature and represents only a small percentage of your TAN. Ammonia becomes ammonium instantly and vice versa as the ammonia molecules become ionized or deionized as the pH/temp fluctuate. Your percentage of toxic ammonia increases with both pH and Temperature.
Free ammonia NH3 poisons your fish with prolonged exposure to 0.02ppm or higher, and is actively harmful and causing gill burn at levels of .05ppm.
This excellent forum post has my favorite chart to determine your level of toxic ammonia. Some math is required, so grab your calculator.
Use the chart to find your pH and tank temperature. Now take that number, and multiply it by your ppm ammonia reading. This is the amount of toxic ammonia in your tank in ppm. If you’re under .02ppm Free Ammonia NH3, your fish are going to be fine. If over .02, I would suggest a water change. Remember that your factor will change if your temperature or pH change, with your toxic ammonia increasing if temp or pH go up. In a case of emergency, temporarily lowering your temperature by a degree or two can make a big difference in your ammonia toxicity.
Calculating The Toxicity Of Ammonia In Freshwater - Tropical Discussion - Tropical Fish Forums
One important thing to know is that the beneficial bacteria will eat EITHER NH3 or NH4. BOTH forms are “food” and will continue your cycle. Scientifically the bacteria does not care or distinguish (much) between them. It will eat the NH3 first, but in the absence of NH3 it will eat NH4. So there is no need to aim for a specific free ammonia percentage for cycling purposes.
Understanding Ammonia Readings | The Fish Lab