Water Chemistry & Filtration

Information covering Water Chemistry and Aquarium Filtration.

I. Aquarium Microbes, Part 1: Nitrification

Aquarium Microbes

Part 1:  Nitrification

What do you keep in your tanks?  A big school of Tetras?  A pair of Cichlids?  A few billion bacteria?  Don’t gag.  The “bugs” are the most numerous things in our tanks and are ultimately responsible for our success if we are to keep our fish alive and healthy.  Every solid surface in our tanks has a biofilm on it, of bacteria, algae, etc., composed of whatever type(s) of microorganism that finds that surface and adjacent water conditions hospitable.  These bugs are not the enemy or in any way unwelcome.  They aid us in the upkeep and function of the micro-ecologies needed to make our tanks stable and safe for our wet pets.

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II. Aquarium Microbes, Part 2: Other small critters

Aquarium Microbes

Part 2: Other small critters

In part 1, I talked about the bacteria that handle the nitrogenous wastes from the fish. Fine, ammonia is dangerous in tanks. But ammonia is just one waste product. What about all the other things?

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III. Fishless Cycling

How to prepare a tank for fish without using livestock

Fishless cycling, as the name suggests, is the method of cycling a tank without using fish. Since we are not using fish, it is the most humane way to cycle a tank. Toxic ammonia and nitrite go unmetabolized during the start of any cycle, causing damage to livestock. The ammonia burns the fish’s gills, eyes, fins, skin, etc, while nitrites decrease oxygen levels in the fish’s blood, causing the fish to suffocate. (» Click here to read the rest of this article…)

IV. EMERGENCY: How to Quickly Cycle a New Tank

Help Me!
“Help me! I recently set up a fish tank and just bought a new puffer (or other fish), but now it’s dying on me!”

Did you just set up a tank within the last 2 months, went to the store and purchased a puffer (or another fish), brought them home, and now they are looking like they are dying?  If so, you are probably suffering from an uncycled tank.

You need to take action IMMEDIATE or you puffer/fish will be dead before the day is over!

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V. You & Chlorine or Chloramines

You & Chlorine or Chloramines


In the United States, most of us get our water for home and aquarium use from our taps. Our taps are supplied with water by a local community, city, or area utility. Those utilities are highly regulated by state and local governments, which are in turn under regulation by the EPA, the Environmental Protection Agency of our federal government. The EPA sets the rules under which our local utilities operate. They define what agents are used to process and disinfect our water supply, and how much of the agent can or must be used. (» Click here to read the rest of this article…)

VI. Considerations in Fishless Cycling

Considerations in Fishless Cycling

Some years ago Dr. Chris Cow, an organic chemist and hobbyist, developed a hobby-level technique for establishing that part of the nitrogen cycle important to our tanks without using and abusing live fish. Not the original articles (that site no longer exists), but a good retrospective exists at:


Chris (a.k.a. Nomad) shared his technique with others on a forum that had a number of experienced hobbyists. Several of those served as beta-testers of the technique, and were quite impressed with how well it worked. That core group started popularizing the technique on the other forums they visited, and the rest is history. Cycling without fish was not novel, several variants had existed for years prior to that time. Some of those variants required knowledge of chemistry and either access to a laboratory or an exceptionally well-equipped home lab, or were completely uncontrolled and frequently smelly. Chis’ technique was and is a better fit with hobby materials and required no special lab equipment, only patience and persistence.
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VII. Brown Algae, Diatoms In Freshwater Tanks by Robert T. Ricketts, a.k.a. RTR

Diatoms are very common algae (yes, they really are algae) in the world. They occur in freshwater, brackish water, seawater, soils, and damp exposed (emerse) situations. They have yellow-brown photosynthetic pigments, so most forms appear brownish to us. In tanks, mostly we see diatoms on lighted surfaces such as the tank walls, décor (rocks, ceramics, plastics, substrate, etc.) and as coatings on plants (either live or artificial). In freshwater (FW) they are generally unicellular, single cells, but in marine environments can have much more complex colonial forms. (» Click here to read the rest of this article…)

VIII. The Salt of the Earth, the Salt from the Sea . . .

The Salt of the Earth, the Salt from the Sea . . .

We say (or at least my grandmother said) that someone is “worth their salt” or perhaps “not worth their salt”, meaning that the person under discussion justifies their existence (or not) by their actions. Can we apply this same sort of value system to the mineral in question itself? Is salt (sodium chloride, NaCl) worth its salt in the freshwater aquarium? Disclaimers are needed first: This is my personal opinion, not the official doctrine of this site, but just me, the cranky old fogy who has rather strong opinions on a number of fish-keeping topics. (» Click here to read the rest of this article…)

VIIII. Veggie Filters

Vegetable Filters

It is generally accepted that healthy plants have a beneficial effect on the water conditions in fish tanks. They absorb minerals including some metabolic waste products from the water, converting these into plant mass. So these may be considered a form of biofiltration. The other mineral ions that they absorb and use could be considered a form of chemical filtration. During their lighted period they adsorb carbon dioxide (CO2), produce oxygen (O2) and submerse plants release excess oxygen into the water, so are also a form of aeration. If the water is not oxygen-saturated, there is no visible evidence of this. In oxygen-saturated conditions, very small bubbles of O2 will form at the leaf surface and be released- this is the “pearling” plant tank growers point to with pride as evidence of strong healthy metabolism in the plants. In the dark they do use oxygen from the water (and release carbon dioxide), but they do not use as much as they produced in the prior light period. So if we accept all that, it is reasonable to want to have plants in our tanks, not just for aesthetic enhancement, or even for refuge for the fish, but for the benefits they can provide to the water quality and thus to our fish. (» Click here to read the rest of this article…)