The “Cure” for Ammonia issues in a pond or aquarium is BIOSEEDING. This is the simple (it is simple) transplant of beneficial germs and microbes from a natural body of water, or an established fish system, into the immature system which lacks those organisms.

What organisms are lacking?

How do I do “Bioseeding“?

About Ammonia as a Fish Killer

Ammonia: Most Common Killer of New Fish

– By Dr. Erik Johnson
Ammonia is the primary waste product of fish, excreted primarily through the gill tissue, but to a lesser extent via the kidney. Ammonia can also accumulate from the decay of fish tissues, food and other organic debris derived from protein. Ammonia accumulations cause reddening of the skin and disability of the gills by its direct caustic effect on these surfaces. Fish suffering in water with high ammonia accumulations will isolate themselves, lie on the bottom, clamp their fins, secrete excess slime, and are much more susceptible to parasitic and bacterial infection.

Ammonia is a big problem in new systems because the bacteria that would naturally dissolve ammonia are not established, see discussion of cycle. As well, even in established systems, ammonia may accumulate in springtime when the water is cold but fish are eating, because filter bacteria have not emerged usefully from hibernation.

Ammonia ionizes below pH 7.4 to Ammonium – and so in its ionized state is less toxic to fish.
Above pH 8.0 most ammonia is ionized, and so becomes more toxic. Care should be taken not to increase th pH of a system if ammonia is present but the need to drop the pH or restrict oxygenation to tanks of fish to keep pH down is an overrated aberration in the literature.

Treatment: Water changes and management of the pH near neutral will go a long way to cutting losses from Ammonias, ancillary, less useful modes of Ammonia management include the use of the various water conditioners that bind ammonia, and the application of rechargeable Zeolites to the system filter. I am still going to tell you that time and water changes are the two mainstays, however.
Water that is warm, high in pH or deprived of oxygen will have an enhanced toxicity when ammonias are accumulating. These are all important considerations as we try to interpret the varying symptomatology of fish at the same ammonia level, for example, but are affected very differently.

You will never have to worry about Ammonia if you use a drip irrigation system for constant water replacement at about 10-20% per week.

More about ammonia

Ammonia – Understand this! – by Doc Johnson
Ammonia is the first waste product of your fish. It is often the cause of your first mortalities in new facilities and new ponds. There is a simple test to measure the levels. I am a big fan of Kent’s Ammonia Detox to reduce the toxicity of ammonia, and of Enviro Reps BRF13A (Ammo Down) for the seeding of beneficial bacteria to reduce the ammonia on the long term. Bioseeding may be the most effective method of all, when possible, and AP’s AmmoLock is great. I do not like Amquel. At all.

1. Made from rotting fish wastes/urine/food
2. Tested with Nessler’s Drop Type tests
3. After (the regrettable) addition of aldehydes such as Formalin or Ammonia-binder agents, test with Salicylate reagent tests.
4. Ammonia causes redness of fins, general poor health, excess mucus production, flashing, and by chronic auto-intoxication: Pinecone disease.
5. Ammonia is more toxic at pH above 8.0
6. Ammonia is directly irritating to fish gills and tissues
7. Ammonia is removed from the environment by beneficial bacteria called “Nitrosomonas”.
8. You can control Ammonia with partial water changes or addition of Zeolites.

I discourage the use of chemicals for Ammonia binding. All but a few of them contain aldehydes (glutaraldehyde) which are guilty of binding oxygen and irritating the fish.

Wet dry filtration (versus submerged media) is very superior for supporting nitrifying bacteria.
I will upload a VERY lengthy discussion of Ammonia in *doc format please check the downloads section.
There will also be a pretty-rare document there showing Gratzek’s research on my favorite ammonia binder, Ammolock II

Additional notes:
“First of all, because it is foiled by fewer organic molecules, let’s establish that Salicylate test kits are superior to Nessler’s tests. Still, Ammonia testing can present a problem. You may not know that dechlorinator can zero-out your ammonia test. The reason is that in the salicylate test kit, chloride ions provide a reagent. Ample dehlorinator and other ammonia binders will zero out this free chlorine reagent and show you a zero test. The only way to be sure that the Ammonia is truly bound up is by “live-tissue cell culture histopathology”. Cells are bathed in test-water and then examined for tell-tale signs of Ammonia damage. The only company that has done this so far is Aquarium Pharmaceuticals who used Drs Lukert and Gratzek at UGA. This Ammonia binder does not contain any aldehydes. Even the so-called “Sulfide Ion” binders are often nothing but Formaldehyde-bi-sulfite (rongalite) which is incredibly unstable.” Doc Johnson