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Aquarium Science Series: Water Chemistry without the Che-misery

Posted by Augusta Hosmer on

A Huge Guide to Freshwater Aquarium pH, Dissolved Oxygen, Nitrites/Nitrates/Ammonia, Water Hardness, and All the Molecules Bouncing Around Between Your Fish - without Feeling Lost or Like You Want to Fall Asleep in Class

"This 8 oz bottle will prevent and cure all fish diseases, fix all your water, grow a tank-wide bacteria colony in 7.2 minutes, and bring your childhood goldfish back from the dead for $42.99! Ignore the other 600 8oz bottles that say the exact same thing!" is what it feels like walking down an aquarium aisle these days. 

Before you go into debt buying products that may or may not help your setup to try and make your water perfect, you should learn what they're claiming to alter. There are some great ones on the market, but knowing how, if, and when to use them is important. So, welcome to part one of Dustin's Fishtanks Aquarium Science Series!

This post will go into detail on aquarium water quality and water chemistry without your needing a science degree to use it. This will definitely be a longer read than some of the other posts because there are so many things you can test your water for, but you can skip to the sections you need or read the bold, "too long, didn't read" lines. Other blog posts will dive into aquarium botany, fish/invertebrate biology, and more, so be sure to check back in! 

Until then, let's get chemical. 


Aquarium Chemistry Overview: Easy Vocab and How to Approach All this Information

Chemistry Vocab/Basics

We'll go into the more specific ones like pH in their respective sections. But overall: 

  • Atoms - the smallest pieces that make up everything we can touch. Made up of even smaller bits we won't torture you with called protons, neutrons, and electrons. For dealing with tanks, just understand the number of protons, neutrons, and electrons are different in every chemical and that makes chemicals behave and interact with each other in different ways. As long as you get opposites attract (protons are positive and electrons are negative) you're good. Also, some atoms are more stable than others. 
A simplified diagram of an atom showing protons, neutrons, and electrons
  • The big one: chemical. It's turned into a media buzz word, but it's not inherently good or bad. They're just substances with the same makeup, and can be large and complex or as simple as a single atom. They can be solid, liquid, gas, etc. and can come together to make things. If it has mass, it's chemical. That's it. Some chemicals are harmful; some chemicals are essential for life. If you ever see a water company claiming their water is chemical free, buy water from someone better - water is a chemical. You are chemicals. Everything around you is chemicals. 
  • Elements - The simplest chemicals and the building blocks of molecules (groups of two or more element atoms - can be from one or more elements. One water molecule has 2 hydrogen atoms and 1 oxygen atom (H2O)). Some examples of elements you might recognize: nitrogen, phosphorus, oxygen, iron, etc. Made from only one type of atom. 
  • Ions - atoms or molecules with an electric charge (because there are different numbers of positive protons and negative electrons)
  • Chemical bonds, binding, etc. - There are lots of different types of chemical bonds we won't bore you with, but this is just how chemicals/atoms join together. Some chemicals are more likely to bond with each other than others.
  • Solute - substance dissolved in another substance (e.g. salt in aquarium water would be the solute, while the water would be the solvent)
  • Solvent - the substance that dissolves the solute
  • Parts per million (ppm) - unit of measurement for a lot of water parameters. It's exactly what it sounds like: parts of solute per million parts of solvent. Think of it like percents (parts per 100) but on an even smaller scale. It's also written as milligrams (mg) per liter (L) or mg/L. So using the saltwater example again, if you had one milligram of salt in a liter (about a quarter gallon) of water, you'd have 1ppm salt. That should give you an indicator of how small some of these changes in your tank are. 


Approaching Aquarium Water Quality without Losing Your Mind

"This is fine" Dog sitting in a house on fire meme

Actual footage of a beginner realizing how many things you can test your water for

It's easy to fall on the extreme ends of maintaining water because there are so many factors at play it feels overwhelming. Some folks take one look at all this, nope the heck out of there, go buy a betta that could probably live in a toilet, and never test water again. Others get so obsessed with details they age like the guy at the end of Indiana Jones and the Last Crusade every time they test their water. We've had the most success in the middle: knowing what's going on and what to watch out for, but also knowing when to just let your tank do its thing. 

Instead of coming at water quality like you have to meet every exact numerical requirement by species and if you don't you're a terrible hobbyist and abusing your fish, realize three things. One: most recommended pH's, temps, etc. come in ranges for a reason - animals & plants adapt. Two: an aquarium is a dynamic environment. If by some miracle you manage to get every single parameter at exactly the values you want, those can change in a matter of minutes and still not be harmful. Every piece of your aquarium affects every other piece, so you shouldn't approach maintaining any of these things in isolation. Looking at it hollistically for your unique setup is healthier for your tank - and for you, because seriously, the last few years have been stressful enough without adding fishtanks to your therapy list. And three: several of these parameters are only major concerns in extremes in most setups, and we'll tell you which ones are which. 

Also: you can test water for a million different things. It doesn't mean you need to, and we can't get to them all. So we'll discuss the ones that come up the most.

6 discus fish in a planted aquarium

Discus, which require you to worry about different water parameters than most other popular species

Overall Tips/Tricks for Aquarium Water Chemistry: 

1) Some of these parameters will affect certain species more than others, so adapt what you worry about to your stock (e.g. Discus prefer higher temp, lower pH environments, so you'll monitor pH more than you would with a zebra danio). Research the ranges your fish and plants like. For recommendations on aquarium plants that thrive in extremes (low pH, low temps, etc.), check out the previous blog post on "EXTREME Aquarium Plants."
2) Do regular water testing/water changes in appropriate amounts - don't go too big or too small. 
3) Understand bigger tanks are harder to alter than smaller tanks (click here for a blog on this for more info!
4) Make big changes gradually to avoid shocking your fish - consistency is more important than exact numbers. But smaller changes? Your chemistry fluctuates all day. The fish will be fine. 


Why is Water Quality Important in your Fish Tank? 

Good water quality is the best way to prevent fish stress, illness, and death - that's the main reason. Maintaining the right parameters also helps aquarium plants grow more easily (which actually help maintain your water quality). Keeping the water chemistry in appropriate ranges also keeps beneficial bacteria in your tank alive and makes your maintenance a lot easier. 


For the following, Meh = be aware of it, test it, don't worry about numbers too much unless there's an extreme/your fish or plants are way out of their recommended range. Worry = if you don't maintain this, no matter what species you have, your fish will die (Again, these guidelines will change depending on specific species, but for general purposes).

pH, KH, GH, Acidity, Alkalinity, Water Hardness/Softness - What's the Difference? 

How worried should you be about pH/Hardness: Meh (unless you have discus or other acid-loving fish, or plants like Anubias that hate soft water)

"What should my aquarium pH be?" This is one of the most frequently asked questions about water parameters. And honestly: pH is something you probably won't need to mess with too much. It's easier to screw up than change safely. Most freshwater fish prefer a pH of 6.5-8.0. If you're trying to breed certain species, though, it becomes more important. pH naturally cycles and fluctuates over time. 

pH scale, showing the pH of common items (bleach pH=13, lemon juice, vinegar pH=2)

The pH Scale (fair use image from the EPA and the United States Geological Survey)

pH and all the other terms in this heading get muddled together because they're closely related, but no, they aren't the same. pH is just a measure of how acidic or basic (not acidic) a chemical is. Bases can neutralize acids (positive and negative cancel out) - remember, opposites attract. How is that determined? We mentioned in the vocab section that ions are charged atoms.

An acidic substance, simply, has more positively charged hydrogen ions and can donate the positively charged protons to a substance with a negative charge (like a base). A base has more negatively charged hydroxide (OH-) ions and can accept positive charges (from a substance like an acid). That's where "pH" comes from: it stands for "potential hydrogen."

This ability/concentration is measured on the pH scale between 0 and 14, where lower (<7) is acidic, higher (>7) is basic, and 7 is neutral (like pure water).

So what's the difference between pH and alkalinity? Alkalinity is how effectively water resists changing pH. So high alkalinity would mean a less drastic drop in pH if you dumped some acid in there, and we know we want stability more than anything. How's it do that? Higher concentrations of minerals (bicarbonate/carbonate). Alkalinity is used synonymously with temporary hardness or KH (carbonate hardness), at least in the aquarium hobby...which transitions us into water hardness. 

Limescale buildup on an aquarium

If you ever see buildup like this on your tank, it's called limescale. It's caused by calcium in hard water and isn't harmful.

Hard water has high mineral content - plants usually love it. Hardness is broken down into the KH we talked about above (which deals with carbonate/bicarbonate) and general hardness/total hardness (GH, which measures the minerals calcium and magnesium). If you live in a place where everyone says they have hard water, they're usually talking GH.

Also, common misconception: strong acids are not automatically more dangerous than strong bases. Battery acid is a strong acid, and bleach is a strong base. You wouldn't want to drink either. 

The Nitrogen Cycle in the Aquarium - Ammonia, Nitrites, Nitrates, Beneficial Bacteria

How worried should you be about nitrates: Meh
How worried should you be about ammonia/nitrites: Worry

Ever heard of someone cycling a tank without knowing what it means? Here the nitrogen cycle, explained:

The simplest way to break down the nitrogen cycle is fish waste/decaying plants/dead fish/decomposing food from overfeeding/ammonium chloride/etc.--> ammonium (NH4+) --> nitrites (NO2-) -->nitrates (NO3-). This transformation occurs because of benefcial bacteria species (Nitrospira and nitrosomonas in particular). The end product, nitrates, will not harm your fish unless they're present in large amounts, but nitrites and ammonia can be deadly. So cycling your tank to establish a bacterial ecosystem/bacterial filtration (which can take several weeks to several months depending on how you do it) is incredibly important for fish health.

A simplified diagram of the nitrogen cycle in the aquarium


If your tank is cycled properly, there should be 0ppm nitrites and 0ppm ammonia. Nitrates will vary, but generally shouldn't get above 10ppm (even lower for sensitive species) over an extended period of time.

It's a common misconception that all ammonia is created equal in an aquarium. However, there are actually multiple forms circulating in the water column, and one form is more toxic than the other. Though all ammonia is toxic, toxicity is influenced by pH and the form the ammonia takes. Un-ionized (not charged) ammonia (NH3) is more toxic at a higher pH, and ionized ammonia (NH4+) is less toxic at a lower pH. 

Aquarium plants are a great way to filter ammonia and nitrates, because they can utilize both as nitrogen sources and nitrogen is an essential plant nutrient (note they cannot utilize nitrites as a nitrogen source). 

Also, common misconception with this section: more mechanical filtration/surface area by itself does not lower ammonia levels. That's what the biological filtration (bacteria) you get from cycling does. Adding things like ceramic rings, etc. that provide more surface area for bacteria to grow can be great if you have more ammonia than your current biological filtration can handle and you want to grow more bacteria to counter that (doesn't happen often). But if the bacteria is already filtering all your ammonia, adding things to the tank is ultimately a waste of money. The ammonia is the bacteria's "food;" the gravel, sponges, rings, etc. are just where it can live. 


How worried should you be: Worry

We have water dechlorinator for a reason: chlorine is a fish terminator. Even tiny amounts can cause major health problems for your fish and invertebrates and can massacre beneficial bacteria. There should be 0 ppm chlorine in your tank.

Chlorine comes in tap water in two forms: chlorine or chloramine. Chloramine, as the name suggests, contains chlorine and ammonia and is even more harmful to fish than straight up chlorine - how's that for something you want nowhere near your tank? Some dechlorinating products tackle one form or the other, and some do both. If you're not sure, your water company is required by law to tell you what is in your water, so you can look it up or call and ask. Or, you can just get a product that does both and move on.

Three popular water dechlorinator product bottles: API, Seachem Prime, and Tetra AquaSafe

As long as you're dechlorinating the water you add to your tank, following dosing instructions, and thoroughly rinsing aquariums you've cleaned with diluted bleach, you shouldn't run into a lot of chlorine problems. 

NOTE: Many water conditioners for chlorine also claim to detoxify ammonia, nitrites, heavy metals, etc. This is the source of an enormous debate, with poorly designed "experiments" on both sides across a wide array of expertise claiming to "prove" whether or not they work. Frustratingly, many of even the top brands will not disclose specific chemical/active ingredient information or studies, claiming trade secrets. Seachem has responded with studies regarding a few of their other products after complaints about this, and I'm hopeful they and others will come forward with actual data on this, soon.

This is not to say one way or the other these products don't do what they claim (because they DO work to dechlorinate water), but until we get more evidence, take their assertions with a grain of salt (pun intended). Manage nitrogen-based chemicals other ways, like with proper cycling/water changes. Not a conspiracy theorist (I've used all of the ones in the pic and several others for chlorine) but I am a skeptic to both sides of the argument when the only experiments I find are on hobby forums without clear methodology. 

Dissolved Oxygen (DO)

How worried should you be: Worry

If your fish and plants can't breathe, it really doesn't matter how perfect the rest of your setup is. Dissolved oxygen is...well...dissolved oxygen - it's a measure of how much oxygen there is in water in ppm. Fortunately, it's easy to get going and maintain. Most people are surprised to learn fish can't just breathe the oxygen in water (the O in the H2O molecule). But the oxygen atom is chemically bound to the hydrogen atoms in a way that it isn't any more available to your fish than it is to you when you swim. 

An Aquarium Air Pump

An Aquarium Air Pump - not as good at producing DO as surface agitation, but still useful

Air pumps and consistent water surface agitation (the most important) are usually enough to provide good DO for your fish. You can also use live plants in your tank to increase DO, because oxygen is a byproduct of photosynthesis. Surface agitation (like with a power filter) will cause some CO2 loss as well, but you can manage this how you need to (more details below). DO is often lower at the bottom of the water column, so if you have a tall/vertical tank, make sure you're getting enough gas exchange throughout. Most species need at least 5ppm DO, though you probably won't have to test for it so much as watch your fish for signs of hypoxia (lack of oxygen) like decreased appetite, labored breathing, and lethargy.

DO is also very important for beneficial bacteria that carry out the nitrogen cycle because this bacteria is aerobic (reaction can only take place/the bacteria can only live in the presence of oxygen).

Hornwort, a green aquarium plant with fine, needle-like leaves

Hornwort, a great plant species for producing DO

It's a common fear heavily planted tanks will consume too much oxygen when they're in the dark and "suck oxygen away from your fish." But unless you're ONLY relying on aquarium plants for your DO, don't sweat it. Yes, plants will use oxygen during respiration, especially at night when they don't have light to photosynthesize. But it's in small enough amounts that if you have a DO source elsewhere, it's highly unlikely to cause problems. 

On that note, some plant species are better at filtering your water and producing oxygen than others. Hornwort (Ceratophyllum demersum, AKA coontail) and Anacharis/Elodea (aka water weeds) are amazing at it. 


Carbon Dioxide (CO2)

 How worried should you be: meh (unless you've got plants)

CO2 is normally not an enormous concern as long as you aren't overstocked and have adequate aeration/DO. Most people never test for it. However, plants need CO2 to photosynthesize, so if you have a heavy plant load or plants that can be difficult to grow, you want to make sure they have enough to thrive. If your fish aren't producing enough, you can supplement it with a CO2 injection system or with a liquid CO2 supplement. Just be aware that too much CO2 can affect your pH, and excess/deficient CO2 alongside other imbalances in your tank can lead to an algae bloom.

Dustin's Fishtanks' Liquid CO2 supplement

Dustin's Fishtanks Liquid CO2 Supplement

How it All Fits Together

We mentioned up above that aquariums are dynamic: all the pieces affect each other - which is why I wrote this in a giant guide instead of breaking it out section by section. If you remember nothing else, the crux of keeping an aquarium happy is balance. So, here's how altering one changes the rest. 

  • Temperature (affects all chemical reactions): higher temp=lower DO; VERY slight changes of alkalinity/KH not worth worrying about; higher temp causes lower pH readings but doesn't alter actual pH/acidity, so you have to correct for temp to get an accurate read; chlorine is eliminated more quickly in higher temps; increased temp = increased ammonia toxicity
  • pH: too low pH makes it harder for fish to absorb DO, but it doesn't affect DO levels directly; extreme pH changes alter KH/alkalinity; unionized ammonia (NH3) is a more toxic form of ammonia at high pH and ionized ammonia (NH4+) is a less toxic form of ammonia at a low pH. 
  • Hardness/Alkalinity: Hard water leads to higher pH and higher alkalinity, while soft water usually leads to a lower pH
  • Dissolved Oxygen (DO): does not directly impact pH, but it can indirectly if it's too low, which allows more minerals to dissolve/can affect hardness, alkalinity, pH, etc.; low DO can cause a CO2 increase
  • CO2: high CO2 lowers pH by forming carbonic acid; low CO2 can be detrimental to plants which can affect DO, nitrates, etc; high CO2 makes it harder for fish to transport DO in their blood
  • Chlorine: high Cl can kill bacteria which can lead to increased ammonia/throw off the nitrogen cycle. High Cl also lowers pH
  • Nitrates: just added this to the list after finding a 2021 study indicating excess nitrates (>50ppm for 3 weeks) led to problems with low DO for fish (added the study to the source list if you're interested!)

You know for a science article I'm not just gonna leave without citing some sources - I don't want any old professors tracking me down. So here's some further reading for ya:  

Understanding the General Chemistry of the Planted Aquarium - Seachem/LSS Laboratory

The Importance of Chlorine in Aquariums and Aquaculture - Hanna Instruments

Aquarium Water Quality: pH - Florida Department of Agriculture and Consumer Services

Pond pH and Ammonia Toxicity - State Specialist for Aquaculture/Kentucky State University

Nitrate toxicity to aquatic animals: a review with new data for freshwater invertebrates

Indicators - Dissolved Oxygen - National Aquatic Resource Surveys - EPA

Exposure to Nitrate Increases Susceptibility to Hypoxia in Fish from the University of Chicago Press Journals

Here are the rest of the Aquarium Science Series posts we currently have up, so if you want more, check 'em out: 

Aquarium Science Series Part 2: Basic Aquarium Plant Botany

And for those who learn better with videos, Dustin did a few on water chemistry as well, so give them a watch with the links down below, hit us with questions and suggestions, and tank on!

How to Do Water Changes in a Planted Tank

Dustin's Pissed Off Rant About pH

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