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Freshwater aquarium chemistry is one of few things I consider to be overemphasized in the hobby. It is covered in every book, beginner's or advanced. It is covered in every forum, every store, every aspect of the hobby. However, it is not as important as as most of these sources make it seem.
In freshwater aquariums the most common tests are pH, ammonia, nitrite, nitrate, and hardness. These all need to be understood before an aquarist can understand what actually needs to be tested, altered, and how it can be safely managed.
PH is the measurement of how acidic or alkaline water is. It is measured on a scale of 0 to 14. 7.0 is considered neutral. Below 7.0 is acidic and the closer to 0 the more acidic. Above 7.0 is alkaline, the closer to 14 the more alkaline. The scale is logarithmic, as opposed to linear, and therefore the difference between 5.9 and 6.0 is the same as the difference between 6.0 and 7.0.
The pH that aquarium fish are native to can vary drastically. The Amazon River can be extremely acidic and dark with tannins, what is called 'blackwater', and have a pH of less than 6.0. The land-locked lakes in the Great Rift Valley (such as Lake Malawi and Lake Tanganyika) can be 9.0. These lakes are fed by rivers but have no drain. Because of this all the minerals that end up in them stay in them. As they have built up they have altered the chemistry of these lakes to extremes.
Most fish in the hobby are raised on farms in water much closer to neutral. This means that even if the fish are from waters that are naturally extreme in pH their parents bred in close to neutral water and they grew up in it. Because of this there is a growing trend in the hobby to not alter pH in any way and simply focus on overall water quality. Most aquarists have found it is much better to keep a good water change schedule which will provide high water quality rather than adding products that increase or decrease pH. One major issue with altering pH is that if the product works at all it is usually short term. This means that the aquarist tests the pH and sees that it is 7.5, too high for his tetras, so he adds some product that lowers the pH. He tests it again and sure enough it is down to 6.5 where he wants it. The next day he tests again and sure enough it is back up to 7.5, so he lowers it again. In some cases aquarists add even more pH altering product than recommended and drop it even further, only to have it go back up again. This roller coastering pH is actually much, much more stressful for fish than simply being at a stable pH of 7.5.
There are few safe ways to alter pH, and few situations where it is warranted. Although fish can live and breed in a different pH than they would have in nature, they are native to waters different than the farms they were raised on. Fish evolved in and adapted to water of a specific pH and many aquarists have found that the closer their aquariums are to the natural pH of the fish they are keeping the better the fish do. It may not be extreme, but the fish will have better colors, be more resilient to stress, have fewer health problems overall, and breed even better.
An aquarist should test his pH at least once, ideally before stocking any fish. This can allow him to select fish that are native to water similar to the natural pH of his tap water and aquarium. In my experience although fish can live and even breed in a pH unlike what they would have in nature, an aquarist is more likely to have problems if they choose to keep fish in water that is unlike what they would have in nature. This may not mean they will die quickly, but may not live as long, grow as large, be as colorful, etc. Because of this it is usually better to choose fish that are from water similar to your tap water. So if you have hard water you may want to avoid things like tetras and choose to keep things like barbs, danios, etc. instead.
Most tap water, whether from the city or a well, is neutralized. This means that it is treated to maintain a pH of around 7.0 while it runs through the pipes. This keeps the water from corroding the pipes or leaving deposits that can eventually clog them. However, this neutral pH usually only lasts a day or two. If the water is left out (or in an aquarium) it will return to its natural chemistry. Because of this it is important to test the water in the aquarium or after it has been sitting out for at least a couple days and not fresh out of the tap.
Hardness is a very frequently misunderstood aspect of water chemistry. Part of the confusion is because there are actually two types of hardness, general hardness (GH) and carbonate hardness (KH).
It is important to note that the term 'alkaline' refers to both a higher pH as well as carbonate hardness (KH). This is actually not too misleading since a high alkalinity (hardness) will create a high pH (alkaline water).
GH is a measure of calcium and magnesium ions in the water. This type of hardness is what is usually referred to when discussing hardness in relation to tap water because it effects how well soap lathers, mineral deposits inside pipes, etc. However, KH is of much more importance in aquariums because it controls pH.
KH is a measure of carbonates and bicarbonates, both of which provide buffering capacity which is defined as the ability to resist a change in pH. A high KH means there are a lot of carbonates and bicarbonates dissolved in the water. This will create a high, stable pH that is very resistant to change. This is why the example in the pH section above kept going back up to 7.5 so quickly. This is why I refer to them as pH/KH because they are effectively the same thing.
What this means for aquarists is that if they are having an issue with pH they need to address KH because by doing so they will alter what controls the pH in the first place. If the pH needs to be increased than the KH needs to be increased. This is actually relatively easy and safe. This can be done in many ways. Some people will use crushed coral as a substrate and use reef type rock in an aquarium that will house African rift lake cichlids which are native to the extremely alkaline lakes. An even easier and more effective method is to place crushed coral in media bags in the filter exactly as if it were carbon. This provides better flow than it would receive sitting on the bottom of the tank with at best a fraction of the flow. The crushed coral will slowly dissolve, release carbonates and bicarbonates into the water column, and increase the KH and therefore pH. It should be replaced regularly just like carbon since a biofilm of nitrifying bacteria can develop on the bagged crushed coral which can actually prohibit the crushed coral from dissolving. The other common method of increasing pH/KH is to add products specifically designed to buffer pH to higher levels. These are usually designed for African rift lake cichlids or other fish from alkaline water like goldfish. Some products simply increase the pH while others will buffer it to a specific pH (such as 7.5 or 8.2). There are even products made for specific lakes. One made for cichlids from Lake Tanganyika will buffer the pH as high as 9.0. Others made for Lake Malawi or Lake Victoria will buffer to around 8.2.
If the pH/KH needs to be decreased it can be much harder to do and more dangerous. The problem is that if the water naturally has a higher pH/KH then either it must be diluted or used up. A lower pH/KH also makes the water very unstable and it can take much less to drastically drop the pH, referred to as a crash, and possibly shock or even kill the fish. There are buffers made to lower the pH/KH but in most cases they do not provide a stable pH, and usually not for very long at all. Using peat is one method used to lower pH/KH. It is usually used as a filter media in the filter just like the crushed coral mentioned above. The way peat works is that it releases tannins and tannic acid. These discolor the water to a merky reddish brown and the acid uses up the buffering capacity of the KH, effectively decreasing the KH and therefore pH. However, its effectiveness is greatly reduced and lifespan shortened the higher the natural pH/KH is. The discoloration is also a major eyesore to almost any aquarist. Although the fish may actually prefer it, if the visibility in the aquarium is low and the aquarist can't actually see the fish very well, it makes for a tank that is less than enjoyable. Because of this the peat method is usually reserved for breeding where the needs of the fish are more important the overall look of the tank.
The safest way to lower pH/KH is to dilute the tap water with reverse osmosis (RO) water. RO water is water that is filtered very well so that there is little to nothing in it. Since pure water does not conduct electricity at all, the conductivity, or total dissolved solids (TDS), is used to measure the purity of RO water. Ideally it has a TDS of 0 (there is absolutely nothing in it) but few RO systems can achieve this, at least not for very long. Most RO systems made for drinking water are far from adequate since they only remove some of the TDS. An RO system made for aquarium use will get the water down to 0, or close to it. By using RO water mixed with tap water the KH of the tap water is lowered. So if an aquarist uses half tap and half RO water the KH of the tap will be cut in half. This will very effectively reduce the pH/KH while still preserving enough of what is naturally in the tap water to allow it to remain much more stable than using pure RO water. Using pure RO water is very risky since there is nothing in it to help keep the pH stable. There are products that are supposed to restore some of this beneficial chemistry. However, in my experience none of them do it very well at all and still allow for an unstable pH that can easily crash. Why use pure RO water and spend money on products to help make it a little more stable when your tap water has everything that is needed already in it for free?
Ammonia, Nitrite, and Nitrate:
Ammonia, nitrite, and nitrate are all part of the nitrogen cycle of every aquarium. Fish release ammonia as a nitrogen waste product. There are also bacteria in the aquarium that breakdown fish poop, extra food, and anything else that is rotting in the tank. These also give off ammonia. Ammonia is consumed by a particular type of bacteria that uses ammonia and gives off nitrite. Another type of bacteria consumes nitrite and gives off nitrate. The bacteria that consume ammonia and nitirte are called nitrifying bacteria. They need a lot of oxygen so they develop colonies in the filter where the flow is very high. This flow not only provides the oxygen but their food (ammonia and nitrite) as well.
Effectively all of the nitrifying bacteria are in the filter. Many aquarists have the idea that every surface in the aquarium has nitrifying bacter. Although every surface has the potential to house bacteria, the bacteria will grow best and thrive where the conditions are ideal for them. Just like how humans do not evenly spread out over the surface of the planet, they become highly concentrated where their needs are best met, bacteria do the same. This doesn't mean that other surfaces in the aquarium are sterile by any means, just that effectively all the nitrifying bacteria are in the filter. I haev seen this idea supported very well when I have moved entire setups from one aquarium to another. I moved the fish and filters at the same but did not move anything else (no substrate, decorations, or water). The new setup did not go through any re- or mini-cycle indicating that all the bacteria needed to handle the fish was present in the filters.
Nitrate generally stays in the water. It is only removed by three things: live plants, denitrifying bacteria, and water changes. Live plants consume ammonia, nitrite, and nitrate as their source of nitrogen. Denitrifying bacteria are bacteria that live in anaerobic conditions where there is almost no oxygen. Under these conditions they actually consume nitrate and give off nitrogen gas (dissolved in the water). These conditions are most common on the inside of porous rock where nitrifying bacteria closer to the surface of the rock consume the oxygen. These same conditions can be found in some biological filter medias that are also porous. The best option is water changes since it is the only one that also removes all of the other bad things that build up in aquariums and cause low water quality. The other two methods simply remove the nitrate while leaving all of the other things that lower water quality such as growth inhibiting hormones, dissolved organic compounds, etc. Since we only have test kits for nitrate it is best to rely on water changes to maintain water quality and not to focus on just removing nitrate.
Cycling refers to the process a new aquarium goes through as it develops adequate colonies of nitrifying bacteria that can handle the amount of ammonia and nitrite produced. This can be a dangerous time for fish since the ammonia and nitrite can build up to toxic levels. However, in larger aquariums it is possible for the aquarium to go through what is called a silent cycle. this is when the volume of water is so large and the amount of fish is so low that their waste is so diluted that the ammonia and nitrite never reach harmful levels. Depending on the fish being used the minimum size tank for this to occur is usually 55-75 gallons. However, regardless of the size of the tank and fish the ammonia and nitrite concentrations should still be checked daily for at least the first two weeks a tank is setup to ensure they stay at low, safe levels. Also keep in mind that some fish are much hardier to ammonia and nitrite than others. While some zebra danios may not be stressed at all, a discus in the same conditions could die.
When an aquarium is first setup the bacteria that consume ammonia and nitrite have not established the colonies in the filters that will be needed long term. They are there, they are actually everywhere including in the air, but they need time to develop into the large colonies needed to keep ammonia and nitrite at undetectable levels. Ammonia and nitrite will always be produced in the aquarium, but once the colonies of nitrifying bacteria in the filters have developed ammonia and nitrite should be consumed as quickly as they are produced and therefore are never detectable. The bacteria will automatically grow to colonies that perfectly match the bioload of the aquarium. The bioload is the waste production rate. The bioload will vary based on the mass of fish in the aquarium, the temperature of the water, the amount of food fed, the quality of food being fed, and the cleanliness of the aquarium. The most common problem with ammonia and nitrite occurs when an aquarist has a cycled tank but then drastically increases the bioload very quickly by adding too many fish at one time. This sudden increase in waste production is not matched by the bacteria in the filter yet so the ammonia and/or nitrite concentrations increase. This is called a re- or mini-cycle. A re-cycle can be bad enough to cause severe stress to the fish or even kill them. This makes it vital to stock slowly and safely. There are no rules on how to stock because what an aquarium can safely handle will vary drastically based on the size of the aquarium, how long it has been running, the amount of fish already in the tank, etc.
The most important thing to test is nitrate because it is the best reflection of overall water quality. If the nitrate is maintained at low levels the other bad chemicals that build up are likely to be low as well. Ammonia and nitrite should never be an issue once the tank is cycled. Hardness should only be tested if the pH needs to be adjusted. The pH should be tested once so that the aquarist knows the natural chemistry of his water and can choose fish that better suit it and it should only be altered in specific circumstances and using safe methods.
If an aquarist only has one test kit it should be for nitrate.