Crystal-Clear Water

6.4. Crystal-Clear Water

Perfectly clear, indeed sparkling crystal-clear, water is the nirvana of any aquarium owner. This factor is difficult to quantify. But all experienced aquarium owners know what crystal-clear water is. It is just something you know when you see it.

If you watch the aquarium YouTube or Facebook videos only roughly one in ten of the experienced aquarium owners have water that has that crystal-clear look to it. Most have water with a dull, semi-cloudy look.

What is often missed in this discussion the importance of crystal-clear water. It goes beyond aesthetics. The usual reason the water isn’t crystal-clear is because of heavy numbers of infusoria, algae, bacteria and protozoans. The bacteria are the most problematic.

Great aquarium with “dull” water
Great aquarium with “dull” water

The aquarium above is beautiful but note the ‘dull” water. Also note the lack of either air stone bubbles or “choppy waves” in the aquarium. With a wavemaker or some airstones (i.e. good aeration) this aquarium might well have crystal clear water. I would predict that the fish in this aquarium will be dying at a relatively high rate.

Bacteria and Fish Health

The fish’s immune system is constantly fighting all the bacteria that the gills are exposed to regardless of the type of bacteria. So a lower bacterial count means more immune system resources available for fighting off pathogens. A high bacteria concentration will compromise the immune systems of the fish and can cause any number of disease and pathogen breakouts. All owners of aquariums should strive for crystal-clear water.

If the bacteria count in the water column is low the fish can put all their immune system resource towards keeping pathogens at bay. So fish in bacteria free water are far more healthy that fish in bacteria laden water.

The Key to Good Fish Health is Clean, Clear, Bacteria Free Water

Note that , contrary to popular myth, this does NOT mean water which has a 50% water change done to it once a week.  The only way water changes can compensate for low biofiltration is if the water is changed on the order of 50% to 100% per day. The mechanism is that these water changes reduce the dissolved organic compounds in the water to the point where there is no food source for the organisms that cause cloudy water. Since these organisms do not need a lot of food this requires VERY heavy water changes.

Bucchochromis nototaenia
Bucchochromis nototaenia

Dull water clarity is due mostly to floating bacteria and infusoria feeding on that bacteria. There are three types of bacteria in an aquarium:

  • Floating bacteria that feed on dissolved organic material (so called water column “heterotrophic” bacteria)
  • Surface biofilm and biofloc bacteria that feed on dissolved organic material (so called biofilm and biofloc “heterotrophic” bacteria)
  • Surface biofilm and biofloc bacteria that feed on oxygen, ammonia, nitrite and carbon dioxide (so called biofilm and biofloc “autotrophic” bacteria).

The emphasis in filtration is generally on the third type of bacteria, the autotrophic bacteria. These bacteria are what is normally called “beneficial bacteria”. What is missed in aquarium hobby is the fact that the second type of bacteria, the biofilm and biofloc heterotrophic bacteria, are also beneficial bacteria. This group of bacteria is the key to crystal clear water.

Further information on the topic of bacteria in the water column can be had by clicking the following link:

4.3. Free Floating Bacteria

Crystal clear water in an aquarium
Crystal clear water in an aquarium

Requirements for Crystal Clear Water

Crystal clear water needs four things:

  • Filter media surface area
  • High filter media flow rate
  • A “mature” filter
  • Good aeration

Surface Area: Elsewhere we determine experimentally that 100 ft² (9,29 m²) of surface area per pound (454 gram) of fish is required for crystal clear water. This is a very important factor:

For Healthy Fish and Crystal Clear Water Have 100 ft² (9,29 m²) of Surface Area Minimum per Pound (454 gram) of Fish

It is also important to note that this same testing determined that ammonia oxidation only requires 5 ft² (0,465 m²) per pound (454 gram) of fish. So ammonia oxidation is easy to achieve while crystal clear water is difficult to achieve.

Flow: The first two types of bacteria (the heterotrophic bacteria) can double in population every thirty minutes to an hour. So flow and water turn-over becomes a factor. This is where water turnover rate through the filter becomes important. If the water turnover rate is only one times aquarium volume per hour the floating bacteria can multiply freely.

If the water turnover rate is two times per hour the surface biofilm and biofloc bacteria in the filter have a good chance to out-compete the floating bacteria in the aquarium, IF AND ONLY IF there is a huge amount of surface area in the filter media (at least 100 ft² (9,29 m²) for every pound (454 gram) of fish. When the heterotrophic biofilm and biofloc bacteria can out-compete the water column heterotrophic bacteria for food the water column bacteria die, and the water becomes crystal clear.

Copadichromis Nkanda – Virginalis Gold
Copadichromis Nkanda – Virginalis Gold

Media Maturity: In addition, it takes one to four months for a good biofilm/biofloc structure (“brown gunk”) to develop in new filter media. If the media is constantly cleaned this structure may never form. This “brown gunk” is largely beneficial heterotrophic bacteria (“beneficial bacteria ain’t pretty”).

Aeration: Another factor is aeration. For every pound (454 gram) of fish in a tank there should be a minimum of 30 in² (194 cm²) of turbulent water air interface. This can be either “choppy waves” on the surface or lots of bubbles.

So crystal clear water needs several things:

  • At least 100 ft² (9,29 m²) of biomedia surface area per pound (454 gram) of fish
  • At least 2X turnover rate per hour of the aquarium through the filter
  • At least two months of filter operation with no cleaning
  • At least 30 in² (194 cm²) in of turbulent air/water interface per pound (454 gram) of fish
sparkling clear water with fish
sparkling clear water with fish


It is important to note that 100 ft² (9,29 m²) of surface area per pound (454 gram) of fish is just one of four methods that can produce SOMEWHAT clear water. All four methods are:

  • 100 ft² (9,29 m²) of filter media surface area per pound (454 gram) of fish
  • A polishing filter media such as Polyfil (polyester fibers), polyester mats (Pinkie Pads) or 40 ppi foam.
  • A UV setup left on 24/7 kills the algae and infusoria in the water column.
  • 50% to 100% water changes every day

What is important here is the difference between “somewhat” clear and “crystal” clear. “Somewhat” clear isn’t bacteria-free water. It is water where the large visible particles have been filtered out but the microscopic stuff remains. Packed polyester (Polyfil) will filter out 200 micron particles. Most infusoria will be less than 200 microns and bacteria are 2 to 8 microns in size. This “somewhat” clear water can be very unhealthy water.

Nimbochromis venustus
Nimbochromis venustus

Using 100 ft² (9,29 m²) of filter media surface area per pound (454 gram) of fish will produce much clearer water than the other three methods as filtration by lots of surface area and flow will eliminate something called “DOCs”, or dissolved organic compounds.

Dissolved organic compounds come from food and feces and are what bacteria feed on. Polishing filter media and UV don’t eliminate DOCs so they don’t produce as clear of water. Large-scale water changes only eliminate a portion of the dissolved organic compounds as feces and decaying food are producing DOCs 24/7.

Aequidens cf. rondoni
Aequidens cf. rondoni

“Natural” Aquariums

Note that pristine waters in nature is often quite turbid. Fish do very well in these turbid waters. But the turbidity is different from what one will see in the TYPICAL aquarium, Turbid water in pristine lakes is loaded with BROWN OR GREEN organic detritus (including very tiny brown detritus and green algae particles) and lots of various algae, protozoa and metazoa. What it won’t have is large amounts of bacteria or dissolved organic compounds.

Bacteria produce water that looks like someone put a little bit of milk in it. What I call “dull water”. It is very slightly WHITE in color. It is the bacteria which are the problem with cloudy or “dull” aquariums.

Note that there are some YouTube folks, Father Fish and Dan Hiteshew at Everyday Fishkeeping for two, who advocate what they call “natural” tanks. Easily 50% of their tanks are clouded with BROWN detritus and have a somewhat brown color to the “dull” water. They typically don’t have a lot of filtration. But the fish in their tanks appear healthy. Their tanks use the detritus to do the biofiltration. This brown floating detritus is their equivalent of “brown gunk” in the filter of a normal aquarium.

I don’t like the “natural” look and feel crystal clear water in the artificial environment of an aquarium is the better way to go. But that is only my OPINION!

Geophagus brasiliensis - Bahia Red
Geophagus brasiliensis – Bahia Red

More information

For a more in-depth explanation of this click on these links:

6.4.1. Crystal-Clear Water in Depth

6.4.2. Polishing Filtration

Note that this water clarity and fish health issue is extremely important to fish from the blackwater of northern South America like discus, rams, neons, apistos, and uaru. This is covered in some depth in this link:

17.3. Blackwater Fish

Note that there is a huge amount of marketing hype to the effect that Seachem Purigen “polishes water to unparalleled clarity“. Side-by-side testing reveals this to be just “snake oil” marketing hype. This link has the tests in it:

7.4.6. Purigen

Astatotilapia sp 44
Astatotilapia sp 44

Startpage Aquariumscience

Source: – David Bogert

Leave a Reply

Your email address will not be published. Required fields are marked *



News, Updates en Promotions

Would you like to be kept informed of News, Updates and Promotions on the AquaInfo website? Subscribe below!