Water Chemistry

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Dec 9, 2003
Halifax, NS
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The mighty brainchild of our very own Orion Girl...

I was drawn to chemistry for the very reason we all need to be aware of it, all life, everything, is tied to and relies on chemistry. As fish keepers, or aquatic plant growers, we need to have some understanding of water chemistry. This understanding can come from years of experience, finding out what works and what doesn't, or through a more intimate knowledge of what is actually happening. Combining the two is the foundation of successful fish keeping.

It is with the new aquarist in mind that I write this, but hopefully some of the more experienced ones can gain some insight into their own tanks, perhaps fill in pieces of the puzzle that goes: "I know that this works, but why?".

I'll try to break things down into sections for bite sized readings in seperate posts, I hope that that will make some sense of what promises to be a long post. Unless I make some glaring error, please refrain from breaking up the posts.

Thank you so much, happychem! I've made this a sticky, and will keep it there until we get the Articles forum setup. Putting this here to avoid breaking up your post. ;) OG


Dec 9, 2003
Halifax, NS
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Chapter 1 - pH

As a calculus teacher once philosphied, 'we like things to be in factors of 10, because we have 10 fingers'. I'm sure I've terribly altered that quote in my mind over the years, but the concept is the same.

To some degree, pH is an effort in that direction.

Hydrogen ion (H+, "H-plus", aka. proton) covers a very wide range in concentrations. In our water based world, H+ concentrations (abbreviated [H+], square brackets are shorthand for the concentration of what they contain) can span a range from 1-0.00000000000001 moles/L, for a pH range of 1 to 14, respectively. Notice that for the pH 14 you need to "move" the decimal (multiply by 10) 14 times to bring the '1' to the left hand side of the decimal (hint, hint).

A mole is a unit of measurement referring to a fixed number of molecules or atoms. Completely unrelated to the star-nosed animal.

To simplify expressions of [H+], pH (the potential of Hydrogen) was invented.

Where pH = -log(base 10) [H+]

In other words, pH indicates the exponent or the number of times you need to multiply [H+] by 10 to equal 1. If you're unfamiliar with logarithmic functions, it may be helpful to think of it a different way:

[H+] = 10 raised to the power of -pH

The power function just means that 10 is multiplied by itself for the number of times indicated in the exponent, pH. The negative means that after you've multiplied 10 by itself that many times, you then divide 1 by that number.

So a pH of 7 means that the H+ concentration is:
- keep in mind: 10^7 = 10x10x10x10x10x10x10 = 10000000
pH 7 = 10^-7 = 1/10^7 = 0.0000001moles/L H+

I understand that this is all a lot to take in, the most important part for you to grasp is that because [H+] is an exponential function of pH, small changes in pH have big changes in [H+], which is what your tank inhabitants experience.

It's, unfortunately, easy to forget that fact. I've been to seminars where the presenter told us that [H+] only changed a little, while something else was more important, and showed a pH difference of 0.5. What he forgot was that a pH difference of 0.5 actually means that [H+] triples!

I'll add in a take home point: lower pH means higher [H+], or more acidic, higher pH means less acidic or more basic.


Dec 9, 2003
Halifax, NS
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Chapter 2 - "KH" - Carbonate Hardness

This may be one of the most misleading terms in aquaria. The test itself does not measure carbonate hardness, but rather alkalinity.

But perhaps I should first step back to a little acid-base theory.

An acid is defined as anything that will either release a proton (H+, remember) or react with its solvent (water in our case) to produce a proton. A good example of the first is HCl (hydrochloric acid) which dissociates into H+ and Cl-. An example of the second is CO2 (carbon dioxide) which reacts partially with water to form H2CO3 (carbonic acid) which then dissociates, releasing H+. In general terms, an acid is written HA, where H is the H+ which will dissociate and the A- is the rest of whatever molecule, the leftover, if you will. To elaborate, using the HCl example:

HA (HCl) -> (H+) + A- (Cl-, for our example)

A base, in contrast, is a molecule that releases, or reacts with water to produce, OH-. The general shorthand used for this is BOH, which dissociates into B+ (the rest of the molecule) and OH-. One of the most common bases NaOH (sodium hydroxide, in many cleaning solvents and drain cleaners) is a good example:

BOH (NaOH) -> B+ (Na+) + OH-

Now let's add a level of complexity. Acids and bases can be either "strong" or "weak". A strong acid or base is one which will dissociate completely when dissolved.

HA -> (H+) + (A-) in water

A weak acid or base only dissociates partially:
HA <-> (H+) + (A-) (note the different arrow, indicating that the reaction can go both ways)

The extent of the dissociation is defined by the "dissociation constant" written as kd (the d is usually a subscript).
kd = [H+]x[A-]/[HA]

This is how a buffer works. A slightly different compound is added that contains "A-", when H+ increases, instead of changing pH, the extra H+ reacts with the extra A- to form more HA, the pH stays the same. It's not quite as straightforward as that, there's a little more balancing with H+ that needs to be done, but now you know the basic concept.

Okay, I know that this is a lot to swallow, but just hang in there a bit longer.

In an acid dissociation (HA -> H+ + A-) A- is called the conjugate base. The same applies for base dissociations, the B+ is called the conjugate acid.

This is important to know because by definition: The conjugate base of a weak acid is a strong base. Likewise the conjugate acid of a weak base is a strong acid. Give it some thought, look at the equations above and consider what's going on. I know that it seems confusing, but it does make sense when you take your time on it.

Now to the meat.

Alkalinity is the sum of all the strong bases in solution, minus [H+].

The most common strong bases in aquariums are HCO3- (bicarbonate), CO3-- (carbonate) and PO4--- (phosphate).

So when you measure KH, you really measure Alkalinity, which is really:
Alkalinity = [HCO3-] + 2x[CO3--] + 3x[PO4---] + [OH] - [H+]
KH = [HCO3-] + 2x[CO3--] +[OH-] - [H+]

Around pH 7, OH- and H+ concentrations are very similar, so they cancel each other out. Their concentrations are also typically very low (10^-7 at pH 7) whereas the rest are more on the scale of 10^-3, so 10,000 times more concentrated.

In fact, if you work out the concentrations, even PO4 very seldom has much effect. Every ppm of PO4 adds about 0.5ppm KH.

So we can, in most cases, ignore PO4 as well, leaving:
Alkalinity = KH = [HCO3-] + 2x[CO3--] (remember that square brackets = concentration!)

The take home point from all of this is that in our tanks KH is what controls pH. The only way to change pH without affecting KH is by adding a weak acid - such as CO2 (there's your exception to the take home point). Stong acids will decrease both pH and KH, but we're unlikely to be pouring these into our aquaria.


Dec 9, 2003
Halifax, NS
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Chapter 3 - GH, "General Hardness"

The general hardness test tells you the amount of Ca (calcium) and Mg (magnesium) in your water. It uses a chelate, usually EDTA, to 'grab' Ca and Mg and an indicator to show when it's all been grabbed.

A chelate is a big organic molecule designed, either by nature or man, to grab metal molecules of a certain size and charge. The name "chelate" comes from the greek word for "crab" since EDTA, the most common chelate, looks like it has a pair of claws, the EDTA molecule looks something like this (forgive the keyboard drawing):

---/ \---
(for some reason, the bottom left prong keeps sneaking in when I submit, it should be directly below the top one)

For thos interested, EDTA stands for ethelene diamine tetra-acetic acid (I've split up the name to make it easy to read. The ethelene is the midde part, the diamine is an amine (a name you may remember from "chloramine", it means an ammonia group) at each end of the ethelene to make the joint of each claw, and the tetraacetic acid is an acetic acid as each 'finger' in the claw. EDTA is also used to treat lead poisoning since it will grab up lead as well as Ca and Mg.

That's just a little background for you all.

It's good to know how much Ca and Mg is in your water. They play the obvious role in bone formation in vertebrates, teeth if your fish have them, shells for inverts. Plus if you grow live plants, these need Ca and Mg as traces as well. Generally important for life.

However, don't confuse GH with the soft water recommended for fish like tetras. This hardness refers to 'total dissolved solids' (TDS), which the hobbyist cannot easily measure and refers to all the molecules/atoms/ions dissolved in the water. It can be measured using conductivity probes, but these are expensive.

Because of this, water softners do not decrease hardness as fish breeders may desire. Water softners exchange Ca++ and Mg++ for Na+ or K+, but note the charge difference! You cannot build up a charge in the water, so for every Ca++ you remove, you must add 2 Na+, so while your GH test kit may tell you that you have a lower hardness, you've actually increased TDS, you've done the opposite of what you want!

If you want to decrease the TDS of your water, you need to use distilled, deionized (DI) or reverse osmosis (RO) water. All of these are costly, but achievable for the dedicated hobbyist.


Dec 9, 2003
Halifax, NS
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Thanks RTR, I'll watch for typos. I did change the arrows as well, I like it much better with the single dash. The '=' was my clumsy attempt at the equilibium half-arrows. Thank-you everyone for your compliments and encouragement, it means a lot.

Chapter 4 - Concerning Concentration

It should seem fairly obvious to anyone who has ever had to talk about any measure of anything, that having a common system of measurement is crucial to clarity.

Without being trying to be too political, I'm going to come right out and say it, the metric system is a far superior system than the imperial. Remember that 10 finger analogy? Flexibility of units is one of its greatest advantages. No matter what size you're trying to talk about, there's a unit for it. But this is not a thread about metric vs. imperial...

In aquaria, concentrations are measured in ppm, or parts per million. This is a fairly common (if frustratingly so) unit of measurement throughout the environmental sciences. It is supposed to stand for the number of molecules of analyte (your compound of interest) for every million molecules of solvent (water, in our case).

Specifically, this would be uL/L (the u should actually be the greek letter mu, pronounced meeoo, and indicates micro_xxxx, in this case litres, so microlitres of analyte/litre water). Solutions this dilute will have no significant effect on density, so the solution can be considered to have a density of 1g/mL, or 1mg/uL. So we can equate 1ppm with 1mg/L.

This is the biggest problem with ppm or mg/L, since it is by mass, not actual molecules, it's difficult to compare one species to another. For example, 1ppm of ammonia does not translate to 1ppm of nitrate in cycling. You must first take into account the molecular mass of the compounds in question.

For example:
Let us pretend that nitrifiers do not keep any of the nitrogen for ther own growth and simply act as catalysts.
NH3 + O2 -> NO2- + H2O + H+

If you added enough NH3 (ammonia) to bring your tank concentration up by 1ppm, how much NO2- would you expect?

Well first you need to convert NH3 to millequivalents per litre (meq/L)
1ppm=1mg/L / [(17mg/mmol / 1meq/mmol)]= 0.0588meq/L
So now you know that you will produce 0.0588meq/L of NO2, equivalents are nice because you've already taken care of the number of reactant molecules to product molecules, notice that in the balanced reaction, one molecule of ammonia produces one molecule of nitrite. So ammonia is 1eq/mol or 1meq/mmol.
Now we need to convert 0.0588meq/L NO2 to ppm NO2
0.0588meq/L NO2 / 1meq/mmol = 0.0588mmol/L NO2
0.0588mmol/L NO2 * 46mg/mmol = 2.7mg/L NO2 = 2.7ppm NO2

I think my calculations are correct, in any case, the point is demonstrated that ppm is a bit of a clumsy unit since it doesn't allow one to follow a reaction.

However, while it does have that failing, it is a common system of units for us, which, when the chips are down, is the most important part. As long as we're all talking about the same units and we all have the appropriate benchmarks in mind, then we can talk about the concentrations of whatever compound in our water to our hearts' content and we'll all understand each other.

One final note on concentrations. Sometimes the term 'titer' will come up. It simply means the amount of a compound in solution. It comes from the analytical method of 'titration', which I'll discuss in the next chapter to some extent.


Dec 9, 2003
Halifax, NS
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Chapter 5 - Test Kits

Forgive the wait between chapters, I've been a little busy of late (see GCC).

We've done covered pretty heavy stuff so far, so thank-you all for sticking with me. This chapter will be a little lighter, I don't plan on going too in depth into the reactions involved, just some general info. on test kits and how they work.

1 - The salt effect
The first thing that I want to mention is that freshwater and saltwater test kits follow the same reactions, for the most part. I didn't realize this until I was reading my test kits at home about a year ago that they were the same reactions as the analyses that I just set up for the Intro. to Chemical Oceanography lab. The biggest difference in them is something called the 'salt effect'.

When something is dissolved a few things can happen: the molecule can sit, surrounded by solvent, it can dissociate into ions (electrolytes, you may say) supported by the solvent, or it can react with the solvent (as does CO2 and acids and bases in water). When salt dissolves in water, it dissociates into positive (cations, pronounced cat-ion) and negative ions (anions, pronounced anne-ions). These ions do not merely sit there, otherwise the salt would never have dissociated, water molecules arrange themselves around the ions to decrease the charge. Nature doesn't like charges, they represent an imbalance, a localized charge means something is ordered, only through complete disorder can things be perfectly balanced. These water molecules are called the "waters of hydration", they are the water molecules used up to 'hydrate' the salt.

So consider it this way, you have a certain concentration of solute (that which is dissolved) in units of "amount of solute/amount of water". But when there's salt around, some of the water is used up to hydrate the salt. So your solute 'sees' less water, and as far as your test kits are concerned, there concentration is higher. It's not an error, because the salt occupies some of the water, the concentration is higher. This is called the 'salt effect' and it's the biggest difference between salt and freshwater tests.

2 - pH and KH
The two most straightforward tests you'll encounter are pH and KH. The former uses a compound that changes colour called an indicator. Indicators are coloured molecules that react with H+ to gain, lose or change their colour. Remember the dissociation constant, kd? It's the same concept, more H+ present, more indicator will exist as 'HA'. Bromothymol blue is a popular choice for pH levels from low 6's to the low 7's. It has a dull yellow colour in very stongly acidic solutions but begins to change from yellow to green as pH increases from 6 through 7 finally, around 7.6 it is dark blue and remains this colour as pH is increased. There are many indicators, most General Chemistry textbooks will have a full page table listing most of them with a colour band showing their colour change over their effective range.

KH incorporates an acid-base indicator with a strong acid titration. In a titration, a measured volume of a compound with known concentration is added to a known volume of analyte with unknown concentration. It is critical that the reaction between the analyte and the added compound be well known, that way you can say that every X amount of compound that I add is equivalent to Y amount of analyte. If you know how they react, how much you've added, and what volume of unknown you started with, that only leaves one unknown, the amount of analyte in the known volume. And since you know how it reacts with the added compound, you can figure that out! Titration is one of the most robust methods of analysis.

I refer you back to the definition of alkalinity/KH in Chapter 2. Note the presence of H+ in the equation. Remember that the components of KH/alkalinity are all strong bases and will react with a strong acid, removing it. The reaction that we need to know is that one H+ will react with each negative charge from a strong base. You want to add exactly enough H+ to neutralize all the strong bases. How is this done:

Your test kit provides you with a bottle of strong acid, likely HCl, and instructs you to count drops (they've measured the volume of each drop). You fill the test tube up to the little line, so you know the volume of your sample. An indicator (bromothymol blue (btb) is a great one for this purpose) is added which makes a sharp colour change in the presence of excess H+. As soon as the btb changes from dark blue to pale yellow, you know that you've removed every last trace of strong base and now have an excess of H+. So now you have added a known volume of known concentration of a compound that reacts in a known manner with a compound of unknown concentration in a known volume. The equation: C1V1=C2V2 is used to calculate concentration. C1V1 means the concentration of the first solution times the volume of the first solution added. C2 is your unknown concentration and V2 is the known volume. So your alkalinity would be:

Alkalinity = KH = (concentration of H- (as OH- equivalents)x(volume of H+ added)/volume of sample.

3 - Spectrometry
Species such as NH3/NH4+, NO2, NO3 and PO4 (analyte) are measured spectrometrically. Excess amounts of certain chemicals (reagents) are added that form coloured compounds when they react with the analyte. Since the reagents are added in excess, the intensity of the colour produced will depend on the amount of analyte present. Again the volume of analyte is critical.

The chemistry involved is not simple, for those interested in a deeper knowledge of exactly what is going on, the reactions, interferants, industrial methods, reagent prep. and such, I refer you to the excellent treatment:
"Methods of Seawater Analysis" edited by K. Grasshoff, K. Kremling, and M. Ehrhardt, published by Wiley-VCH, 1999.
Standards, solutions of accurately and precisely known concentrations are prepared. These standards of different concentrations are treated the same way as the samples. The intensity of colour produced is a function of concentration, which is known. The intensity is measured by an instrument called a spectrophotometer which measures the amount of light of a certain colour (wavelength) that passes through a sample and compares it to the amount of light that is emitted. This is called absorbance, it has no units and follows my favourite law: The Beer-Lambert law, okay, I just like the first guy involved. ;)

Beer-Lambert sais, that for the appropriate conditions, which are set in the lab:
A (absorbance) = a*b*c (easy to remember, no?)

a is the molecular absorbtivity, it's a molecular property, specific to the coloured compound. a has been measured already, so it's a number that you look up in a text. b is the path length of the cell that contains the sample. Makes sense, the farther the light has to travel through the absorbing compound, the more that will be absorbed, this is fixed in the lab by running all samples through the same cell.

That leaves c, concentration. Since you've got standards of known concentration, you make a plot of A vs. c. a and b are fixed, so you get a straight line relating A to c. Now you run your sample and compare the Abasorbance that you measure to the standard curve, you've now determined concentration.

For all that's involved, spectrometry is one of the easiest and most bulletproof methods of analysis. It does require some initial preparation to ensure that you've accounted for the various requirements of the Beer-Lambert law, but once it's set up, a trained monkey could run the samples. Heck, I've even built a (crappy) spectrophotometer.

But obvioulsy this isn't practical, or economically feasable, for the average hobbyist, so the manufacturers run standard for us and print out the colours for us to compare to. Not something I'd want to try to publish a scientific paper from, but more than sufficient to know what's going on in an aquarium.

One last note of interest. NO3 test kits don't measure NO3, they measure NO2. Those of you with the Hagen/Nutrafin test kits may have noticed that the first two bottles look very similar to the two bottles provided with the NO2 kit, or that the colours are similar. That's because they are identical. The NO3 test uses a chemical called a reducing agent (a chemical which decreases the negative charge of a compound, or for biologists, removes oxygen) to convert NO3 to NO2 (that's the brown glass bottle for the Nutrafin types) then forms the same coloured compound as for NO2.

I can't resist throwing this in: For those very, very few of you out there who are keen on really getting to understand spectromoetry, as well as the optics involved and pretty much an in depth presentation of modern analytical spectrometry, there is no text I've found that is better than:
"Spectromchemical Analysis" by James D. Ingle Jr. and Stanley R. Crouch, published by Prentice Hall. This is not light reading.


Dec 9, 2003
Halifax, NS
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Some educational sites

before I continue, I'm going to insert this tread to give people a place to go that may be a little more in depth or more peripheral than what I'm discussing. I'll try to screen them as best as possible and post new ones as I come across them.

First and formost, the periodic table of the elements. Drag the cursor over an element's symbol and the full name is displayed. Click on the symbol and you're linked to a fact sheet.
To clarify, the table is set up like a matrix. Groups making up columns and rows for the, um, rows. Elements in the same group will have similar chemistry. Size increases with row number.

Here's a good online chem tutorial.

This site had a really good run through of basic nomenclature:
But there are a few clarifications that should be made that the author glosses over:
1 - Only use the prefixes (mono, di, tri, etc.) for non-metal compounds, sodium annd the like count as metals. Imagine a diagonal line passing through Aluminum (Al, number 13) through Polonium (Po, number 84) everything to the left of this line, including those in the line, are metals, so bimolecular compounds containing these don't have prefixes.

2 - Something tricky to get your head around:
Some elements can exist in numerous different oxydation states (charges), see the hypochlorite, chlorite, chlorate, perchlorate example. The suffixes "-ite" is assigned to the lower charge and "-ate" to the upper charge (like nitrite, NO2 and nitrate, NO3).
If there are more than 2 possibilities, prefixes "hypo-" to the lowest and "per-" to the highest are assigned. You porbably could have puzzled it out from his example, but I felt that it should have been stated explicitly.

3 - Parentheses ("used when needed" ;) ) are used to clarify the presence of seperate compounds within the compound you're trying to name. For example, potassium nitrate, KNO3 is fairly straight forward, and we know that it will dissociate into K+ and NO3-. However, calcium nitrate, would be Ca with 2NO3's. But if it was written CaNO32, it would appear that there were 32 oxygens and if it was written CaN2O6, one would be led to believe that the two N's were bound together and that the Ca was tied in there somehow between a pair of O's. So to make clear that it is indeed 2 nitrates in the compound, it is written as: Ca(NO3)2. So read this from the outside in, 2 Nitrates, each have a single negative charge, bonded to a Calcium, with two positive charges. This approach will help to clarify things when (if) you ever run into big, scary names.

Despite my 'clarifications' this is a really good and clear site. I believe that the clarifications were only necessary to make this edible for those who haven't taken General Chemistry, or else took it many years ago and have since forgotten.

If anyone has any other subjects that you'd like clarifications on, let me know and I'll see if there's a site that makes it decently clear or a text that I can recommend.

...and now back to our regularly scheduled programming...


Dec 9, 2003
Halifax, NS
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Chapter 6 - The 7th Element

That would be nitrogen, more specifically, this chapter will deal with the three nitrogen species with which we are all familiar (or are soon to be): ammonia (NH3), nitrite (NO2), and nitrate (NO3). The reason that this chapter, on an undeniably central concept to aquarists, was pushed so far down was because to best explain some of the concepts, it was first necessary to talk about concentrations and measurement techniques.

Specifically, I do not intend to talk about toxicity and cycling so much, these are discussed exhaustively in numerous places.

The first subtopic is of measurement and exchange of information. This will extend my gripe with units of ppm. Although I previously mentioned that the key to units is to have a consistent form in which to present our data to each other, complete with relevant benchmarks to tell us what's a healthy level vs. a dangerous one, ppm is especially cumbersome when it comes to discussing the nitrogen cycle.

Why? Because there are now two ways of looking at things, we measure the compound directly, but do we want to talk about the concentration of ammonia in our tank or the amount of nitrogen in the form of ammonia?

Why, you ask, is the latter relevant? Well, let us take the problem apart piece by piece. First, know that there are two ways to report concentrations of each compound:
ammonia vs. ammonia-nitrogen (NH3-N) or total ammonia nitrogen (TAN)
nitrite vs. nitrite nitrogen (NO2-N)
nitrate vs. nitrate nitrogen (NO3-N)

Back to the question of relevance. Well, with the exception of benchmarks for tank health, the first of each pair tells us nothing about nitrogen chemistry. This is back to the problem of ppm being a mass based unit, 1ppm of NH3 does not produce 1ppm of NO2!

To get around this problem, the second set of terminologies was developed. These strip the compounds down to the element of interest, nitrogen. This looks at the issue from the point of view of the nitrogen atom being oxidized and allows each to be compared directly:
1ppm NH3-N = 1ppm NO2-N = 1ppm NO3-N

But how do we arrive at these values? Well, we go back to molecular mass (these are approximate values):
N = 14g/mol
O = 16g/mol
H = 1g/mol

NH3 = 17g/mol
NO2 = 46g/mol
NO3 = 62g/mol

So, what is the weight ratio between each species and nitrogen?
NH3/N = 17/14 = 1.2
NO2/N = 46/14 = 3.3
NO3/N = 62/14 = 4.4

So to convert your measured concentrations to nitrogen equivalents:
NH3-N = [NH3]/1.2
NO2-N = [NO2]/3.3
NO3-N = [NO3]/4.4

Lets try this out on the example from Chapter 4 where I demonstrated that 1ppm of NH3 would produce about 2.7ppm of NO2.

1ppm NH3/1.2 = 0.83ppm NH3-N = 0.83ppm NO2-N
0.83ppm NO2-N x 3.3 = 2.75ppm NO2 and 3.67ppm NO3.

Well, that makes it all very simple doesn't it? But of course, if we all used molarity, or even better, equivalents, as our base unit of measurement, we wouldn't have to go through all this conversion to start with.

So, if we are going to stick with ppm as our system of units, why don't the kits simply report in units of Nspecies-N instead of having to make the conversion?

Well, there are a few things that come to mind, but most notably is that with the exception of interrelations between the species this is not a very useful unit of measurement. For example, the standards to show the colour change, are prepared gravimetrically. This means that the amount of NH3 (or NO2 or NO3) is weighed on a very precise balance and added to a precisely known mass or volume of water. So simply recording mg/L is convenient, although they would still have to use molecular mass to factor out the Cl in the NH4Cl likely used to prepare the standard. So in short, I'm stumped, I can't really think of a good reason to simply use compound specific ppm, but then, I can't think of a good reason to use ppm instead of molarity to begin with, so there it is.

While 'cycling' is a convenient term, it's derived from a process which does not happen in the aquarium, the nitrogen cycle. In the wild, such as the ocean, there are organisms which cycle nitrogen, both fixing N2 (nitrogen gas) from the atmosphere, converting NH3 to NO3 and others to convert it back to NH3. This doesn't really occur in the aquarium, in facts it's a unidirectional process, fish excrete NH3 (there are other sources as well, like decomposing vegitation and fish scales) and bacteria convert it to NO3. The NO3 is removed through water changes, but is not cycled back to N2.

However, this is advantageous to those of us who do not wish to spend millions of dollars to set up an analytical laboratory to analyse our water.

Fish are not just NH3 factories, their wastes contain all the breakdown products of their food which they did not or could not absorb for their own metabolism, these can be sulfur compounds and organics, neither or which we can measure easily or cheaply. They secrete hormones which while in nature would be flushed out simply remain in the water and build up. None of these are good for the fish but sadly we cannot measure them. But all is not lost. We can measure the NO3 that is produced from the NH3 that they secrete and based on this, we can make a hand-wavey generalisation about the other pollutants in the tank. To my knowledge, no one has actually measured the precise relationship between meausured NO3 from fish secreted NH3 and concentration of fish derived pollutants, but it doesn't matter, we can choose a benchmark NO3 level, like 20ppm and adjust our maintenance and water changes accordingly.

So NO3 is not just the non-toxic (in the short term) end product of 'cycling', it also allows us to have some idea of the level of pollutants in the tank.


Dec 9, 2003
Halifax, NS
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Chapter 7 - Ammonia and ammonium

Ammonia (NH3) vs. ammonium (NH4+) deserved its own chapter. NH4+ is much less toxic than NH3.

Ammonia reacts with water to produce ammonium and OH-, so long as the pH is low enough:

NH3 + H2O <=> (NH4+) + (OH-)

This is an equilibrium reaction, so we recall our dissociation constant, kd. But since this is a base dissociation, it's written kb.


Technically, water should be included; however, since all the situations we will see are dilute solutions, the concentration of water can be said to be constant and is therefore lumped in with the constant.

For 25oC kb for NH3 = 1.75x10^-5 which means 0.0000175.

For those interested in a little meat
math alert
Now you can actually determine for yourself how much of each species is present using this information and pH.

Remember that pH = -log[H+], well, for aqueous solutions (a solution where water is the solvent) pH has a range from 0-14.

pOH is just the opposite. pOH = -log[OH-] = 14 - pH.

So, [OH-] = 10^-(14-pH) (the "^" symbol means "raised to the power of" and is commonly used when exponents aren't available in the typeset.)

Now, using a little algebra, we isolate [NH4+] from the kb equation above:
[NH4+] = {kb/10^-(14-pH)} x [NH3]

Your ammonia test kit measures all the ammonia, regardless of ionization. So your test kit result, let's call it x:
x = [NH3] + [NH4+]

Now we can substitute in our equation from the equilibrium constant and pH:

x = [NH3] + {kb/10^-(14-pH)} x [NH3]

And finally, isolating [NH3]:

[NH3] = test kit measure/{1+kb/10^-(14-pH)}
[NH4+] = test kit measure - [NH3]

and remember that kb = 1.75x10^-5 at 25oC, which is pretty close to average tank temp.

I know that nutrafin test kits have a chart that tells you how much NH3 you have based on the test kit measurement and pH, but it's nice to know where it comes from and to know that you can do the calculation yourself!


Dec 9, 2003
Halifax, NS
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Chapter 8 - Filter inserts

Since this is a chemistry article, I'll be brief on the bio/mechanical inserts. This is not a chapter on filter selection

There are numerous choices for filter media. Most sites (that I've seen) will tell you that you need three types of filtration in your filter: mechanical, biological and chemical.

Mechanical filtration refers to the removal of particles from your water. These can be such things as uneaten food, fish wastes, scales, dead plant matter, etc. If it's small enough to fit into your intake tube and small enough to get caught up in your media, it's subject to mechanical filtration. That said, there are a variety of sponges, foams, and finer media like diatomaceous earth and micron filters that are available to you. Strictly speaking, you can filter out as small a particle as you want, as long as you're willing to spend the money. Know that it's not strictly necessary to remove every tiny bit.

Biological filtration is the single most important type of filtration. The development of a biological filter is what we refer to as cycling. In doing so, filter media is colonized with nitrifying bacteria. The key elements to this are water flow, oxygen, and surface area. The first two are supplied by the filter pump and the last by your media. There exists a variety of products from generic filter sponges to bio-balls that can accomplish this end. The only rule here is go big or go home, fill your filters with as much surface area providing media as you can fit in, and don't rely on the manufacturer's maximum rating, it's overly generous.

Chemical filtration is the addition of various media to your filter to remove "undesireables" from your water. As much as I love chemistry, this type of filtration is simply not necessary in the day to day workings of a well maintained and properly stocked tank. There are three types that I'll discuss here: activated carbon, zeolite, and 'others'.

Activated carbon or charcoal is, as the name indicates, little chunks of carbon. The 'activated' part means that each of these little chunks are littered with holes and crevasses, look at a piece of lava rock to get an idea. These holes greatly increase the surface area provided by the carbon, the importance of this will soon be evident.

Activated carbon (AC) works by a phenomenon called adsorption. This differs from absorption in that nothing as actually sucked into the compound. Simply speaking, absorption does not occur at the molecular level, one molecule can not suck up another the way a sponge suck up water.

Adsorption in a result of intermolecular attraction. Think of your favourite building set, when you build a big structure the pieces in the middle are surrounded by other pieces, supported by them, but the pieces on the outside are left open. A similar occurance happens at the molecular level, atoms (or molecules) inside the structure are stabilized by those around them, but those on the outside are not. While they are satisfied as far as bonding is concerned, there's still this side of them that isn't complete and in this void a short force field exists, other molecules that come into contact with this force field stick to the surface, filling the void. This force of attraction does not propagate through the stuck on molecule because it is not a part of the solid, merely associated with it through a relatively weak force of attraction. So once all the surface is covered in stuck on molecules, no more will be adsorbed. Hence the importance of surface area!

This is wonderful! AC can be used to remove medications, organics and all sorts of undesireables from your tank. But if used regularly all the adsorption sites would be filled within a couple of weeks, depending on the stocking and feeding levels of your tank. So you see that AC can be a wonderfully useful tool for post-medication and for a vacation when you'll be unable to do a water change for a couple weeks. But for general purpose filtration, not terribly useful. As an added downside, if you keep a planted tank, AC will also adsorb chelates, which means it will pull trace elements out of your water. It does not discern one organic compound from another.

Zeolite is used for ammonia removal and is sold under brand names like ammo-lock. For day to day use this is one product that could actually be harmful to use. Much like AC adsorbs organics, zeolite adsorbs NH3. This makes it a very attractive product for people who are afraid of ammonia and especially uninformed consumers and/or new hobbyists. The danger lies in that it does exactly what it promises, it removes ammonia, but this means that it starves NH3-nitrifiers, reducing their colony size. Consequently, NO2-nitrifiers are also deprived of their food. But you've got zeolite, so who needs them, right? Wrong! Again in the same way that AC will become expired after a short time depending on stocking and feeding, as will zeolite. Once the adsorption sites are full, there's no more NH3 removal. Your fish are still producing the same levels as before, but your biological filter is unable to support the bio-load, so you get an NH3 spike and a NO2 spike. It is not a bad product to have for an emergency, something happens (like a well-meaning roomate cleans your filter in chlorinated water) and your bio-filter crashes, but it is not something to be relied on.

Others. I've group the remaining types into a general group because there are simply a limitless number of possible options and the rest are generally less prevalent than the above, for example, products that adsorb phosphates (PO4). As I said, there are limitless possibilities, if there's something that someone decides should not be in a tank, it's easy enough to develop something that will adsorb it or chelate it and stick it to a teflon or silica bead. The bottom line that I want to make clear in all this is that these are generally useless products, or to quote one of my favourite expressions: "a solution in search of a problem". As with all the above chemical filtration media any problem these products propose to remedy can be solved by water changes and proper aquarium care. As with any other hobby, there is work involved to be successful in aquaria. Trying to get around tank maintenance, water changes, proper feeding and stocking by adding products such as special (and expensive) filter media to atank will not only not solve your underlying problem, but in the long run will lead to a lack of success in the hobby.
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