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On this page I have two articles that explain the Nitrogen cycle. The 2nd one is simpler

Water Quality 101

Why Test Water?

New pond syndrome

Establishing and maintaining proper water quality is essential to a healthy pond. Crystal clear water does not guarantee an ideal environment for your fish.

Important!

Tap water contains chloramines and chlorine. They are toxic to fish and will kill them. It also will kill beneficial bacteria. You should always remove chloramines with a dechlorinator that removes it instantly. They are easy and available in most pet stores. This is the most common first mistake people make.

Avoid Deadly New Pond Syndrome!

Many disease outbreaks and fish deaths can be directly linked to stress caused by poor water quality. Improper pH and uncontrolled levels can encourage undesirable alga growth. Inappropriate water hardness and alkalinity can create long-term problems and may prevent the hobbyist from keeping fish active and healthy. Excessive organics can foul the pond and cause fish losses. Maintaining optimum water quality can prevent most diseases. New fish in a new pond will get sick and die due to ammonia and nitrite spikes from an un-cycled biological filter. Regular use of test kits available from pet stores will help you maintain the fish’s natural environment.

What Happens in your Pond?

The introduction of fish, plants and food into your Pond begins a series of processes, collectively known as biological filtration. In biological filtration, naturally present bacteria safely converts wastes into less toxic compounds (See fig.1)  More than 50% of waste produced by fish is in the form of ammonia, the majority of which is secreted through the gills. The remainder of waste, excreted as fecal matter, undergoes a process called Mineralization. Mineralization occurs when heterotrophic bacteria consume fish waste. Decaying plant matter and uneaten food, converting all three to ammonia.

As ammonia levels rise in the water, another group of bacteria Nitrosonomas, feed on the ammonia and convert it to nitrite

You can see that ammonia levels reach a peak and then decline, corresponding to the production of nitrite. Nitrite is consumed by the bacteria Nitrobacter and is converted to nitrate.

 

In Fig. 2, you can see that ammonia levels reach a peak and then decline, corresponding to the production of nitrite.  Nitrite levels reach a peak then are consumed by the bacteria Nitrobacter and converted into nitrate.  New pond syndrome happens at these peaks. Unknowingly the levels are high and fish get sick. This happens in new ponds with excess fish loads or over feeding and a filter that is not working properly.

The end product of the biological filtration process is nitrate.  Conversion normally occurs within 4-6 weeks of setting up a new pond. Nitrate levels will continue to rise unless removed through regular partial water changes or utilized by live plants. Nitrate is much less toxic. It can be used as an indicator that the filter has cycled. It is now safe to add fish. You have avoided New Pond Syndrome the 2nd most deadly and common mistake. What is the first?  Chlorine!

               pH

                                    At a pH below 7,              At a pH of 7,            At a pH above 7,
                                       there are                 which is neutral, there       there are
                                    more Hydrogen           are equal amounts of     more Hydroxide
                                     ions (H+) than         Hydroxide ions (OH-) and   ions (OH-) than
                                    Hydroxide ions (OH-)    Hydrogen ions (H+)     Hydrogen ions (H+)     

             
Acid                                                  Base
                                                         pH 7 is Neutral                                                 Fig. 3

                                                                     

pH is an important factor in your pond. It is responsible for controlling many chemical balances, including the ratio of nontoxic ammonium (NH4+) to toxic ammonia (NH3), and between the nitrite ion (NO2-) and nitrous acid (HNO2). The term pH stands for the power of hydrogen and is a measure of the amount of hydrogen ions present in your water.

The pH scale runs from 0.0 to 14.0 Values of less than 7.0 are acidic, 7.0 is neutral and values greater than 7.0 are basic. (Base/basic has formerly been referred to as alkalinity. Alkalinity is actually a measure of the buffering capacity of water).

Stay above pH 7.0 for best results with Koi
 
pH can "crash" to 5.5 overnight due to fish, plant and bacterial activity without adequate buffering of water - fatalities result
Baking Soda is a good buffer. Check Total Alkalinity before its use, though. (Use one teaspoon per ten gallons if  the TA <100)

pH is a measurement of the free hydrogen ions in the system.

pH is measured on a scale of 1 to 14, but the pH required for life lies between 5.5 and 8.5.

Individual species will have varying demands as far as pH. Ignorance of the requirements of each species will result in the death of the animal in question.

pH impacts fish in several ways.

First, if the pH is too low, a condition within the fish called "Acidosis" results.

Symptoms are anorexia, and then production of excess slime, isolation, and resting on the bottom, finally, streaking of the fins, and death will occur.

If the pH is too high, the fish will produce excess slime, and will gasp at the surface. Losses can be major. "Alkalosis" is hard to reverse once it occurs.

On the other hand, Acidosis is rapidly corrected once the pH is brought up to a suitable range.

IMPORTANT: pH contributes to the toxicity of Ammonia.

At higher pH values, ammonia is more toxic.

Below pH 7.2 most Ammonia is ionized to "Ammonium" and is far less toxic.

This has relevance if you are considering raising the pH in a system with accumulating ammonias.

 

The pH in freshwater should be between 6.0 and 8.4.  It is important to know the pH requirements of the species of fish being kept. Koi are quite happy in a pH of 8.0 and handle higher. Stable levels are sometimes more important than the perfect 7.5. Koi can get uses to a higher pH if it is stable. Do not try to make large changes in pH with treatments. Higher pH makes Ammonia more toxic but if you have no Ammonia you are safe. A sudden pH fall that can kill a whole pond overnight. Low pH can be an indicator of too high a fish or high organic matter. Buffers can be used keep pH stable. Baking soda is used as Buffer.

pH is prone to "fall" in un-buffered systems, and can fall precipitously due to Oxygen consumption, accumulation of Carbon dioxide, decay of fish and other wastes, and the normal activity of nitrifying bacteria which reduce Ammonia to Nitrite.

"Crashes" from a normal pH all the way down to pH 5.5 can occur overnight. At 5.5 the filter bacteria that may have contributed to the crash will shut down, preventing the crash from dropping yet further.

In systems where the pH has been chemically stabilized by any of natural or commercial buffers the pH crash phenomena is not commonly seen.

When "pH Crash" is observed, bring up the pH **rapidly**, not slowly. Would you want to be removed from a smoke-filled room rapidly or slowly?

 

Ammonia

As stated earlier, the majority of fish waste is converted ammonia. Ammonia exists in two forms: as toxic ammonia (NH3), and as the nontoxic ammonium ion (NH4+). At any given time, The amount present in each form is primarily dependent on pH, and to a lesser extent temperature. Ammonia is more toxic at a high pH and high temperature than at a low pH and low temperature. (See Fig. 5)

All of the test procedures used in ammonia testing measure total ammonia, which is a combination of ammonia and ammonium. To properly determine the amount of toxic ammonia, you need to know the pH and temperature of your pond. Utilizing the chart you can easily calculate how much toxic ammonia is present. For example: Upon testing your water you find that there is 2.5 ppm (mg/L) [parts per million or milligrams per liter], total ammonia, the temperature is 75 degrees F and the pH is 8.0. From the chart, you find that the corresponding factor is 0.0502. By multiplying the amount of the total ammonia by this factor, you are able to determine the amount of toxic ammonia is your water:

2.5 ppm ammonia x 0.0502 = 0.1255 toxic ammonia.

pH 72degF
22degC
75degF
24degC
79degF
26degC
82degF
28degC
86degF
30degC
6.2 .0006 .0010 .0011 .0011 .0015
6.4 .0010 .0015 .0016 .0018 .0023
6.6 .0016 .0023 .0025 .0028 .0036
6.8 .0026 .0036 .0040 .0043 .0055
7.0 .0046 .0052 .0060 .0069 .0080
7.2 .0072 .0083 .0096 .0110 .0126
7.4 .0114 .0131 .0150 .0173 .0198
7.6 .0179 .0206 .0236 .0271 .0310
7.8 .0281 .0322 .0370 .0423 .0482
8.0 .0436 .0502 .0574 .0654 .0743
8.2 .0676 .0772 .0880 .0998 .1129
8.4 .1031 .1171 .1326 .1495 .1678

Calculated toxic ammonia levels should not rise above 0.05 ppm, as higher levels can stress the fish and possibly cause gill damage or fish death. Visual signs of ammonia toxicity may include fish gasping at the surface of the water, cloudy eyes and frayed fins. If toxic ammonia levels above 0.05 ppm are present, it is advisable to do a partial water change with water at a pH of 7.0 and reduce feeding. Do not add any more fish until the ammonia levels have decreased.

Most dechlorinators also contain additives that bind ammonia. They can help but, may also mask it from the test. Ammo lock 2 was shown to prevent gill damage others may not. In new ponds ammonia will start to lower in about 2 weeks as the Nitrosomonas bacteria gets established in the filter.  Ammonia levels rise quickly in the fist 4 weeks. This is when New pond syndrome occurs. New fish that were just fine all of a sudden get sick. The hobbyist may try treating the illness and not the cause which is high ammonia. Test for ammonia. 

Nitrite

Nitrite (N02-) is produced from ammonia by Nitrosomonas bacteria. Nitrite is toxic to fish because it interferferes with the fishes ability to use oxygen. Nitrite is also pH dependent. If nitrite is present in your pond and the pH falls below 6.5, the nitrite will start to be converted to nitrous acid, which is also toxic to fish.  If high nitrite levels are present, 1.0 ppm it is advisable to do a partial water change. Do not add any more fish until the nitrite levels have decreased. This is also when new pond syndrome occurs. 3 to 4 weeks after setting up a pond or over cleaning biofilters, ammonia will be zero but nitrite levels will be high. Fish get sick. Test for nitrite.

See fig. 2. Nitrite is more toxic to fish than ammonia and causes gill damage. That’s due to the fact that the Nitrobacker Bacteria develop after Nitrosomonas Bacteria has converted the ammonia into nitrite. It can take 3 to 4 weeks for Nitrosomonas to develop in your filter enough to bring the nitrite levels down to a safe level. Use patience, the first 6 weeks are when you can have the most losses if you are not careful. Test your water and watch the changes in ammonia and nitrite over time. Then you can monitor the levels as you add fish and make changes. If your ammonia or nitrite levels are  high  (any thing above 0.05)  you can lower them to a safer level with a partial water change. If you change too much at once, it can stress your fish and prevent the filters from maturing. Remember to dechlorinate tap water. Chlorine is toxic to fish and the bacteria you are trying to establish in your filter. Adding salt to the water can reduce the toxicity of nitrite. 0.02% is a good amount. Check the article "salt the wonder drug" on this web site for full information.

Nitrate

Nitrate (N03-) is the end product of the nitrogen cycle and is relatively nontoxic. Plants and algae use nitrate as a food source. In freshwater it is recommended that nitrate levels be kept under 60 ppm (mg/L). Levels in excess of 100 ppm can be tolerated, but anything above this level should be avoided. Excessive nitrates will promote the growth of algae and can lead to fish health problems. Nitrate levels can be lowered by regular 10%  to 20% water changes. Plants can lower nitrate levels but you need a lot of special ones like Hyacine or Waterlettuce, which can absorb large amounts of nitrate. Special filters like Trickle Towers, nitrate reactors, and vegetable filters can also help lower levels of nitrate. The presence of nitrate is a sign that the ammonia and nitrite are being broken down. As the nitrite levels fall the nitrate levels should start to rise.

Wait for your biological filter to mature. Test  for ammonia and nitrite. Avoid disaster known as New Pond Syndrome. This will be the single most important thing you do.