Aquarium water is normally clear and colorless, but from time to time it can become cloudy or tinted in color. Unexpected yellow or brownish colored water is usually a sign of trouble afoot, although there are causes that are not a problem. To ensure that your aquarium habitat is safe for your fish, you should investigate yellow or brown water problem promptly to determine the root cause and correct it, if needed.
Bacteria overgrowth, often referred to as bacterial blossom or bloom, will cause cloudiness. In fact, the water may appear to be gray or milky, but the bacteria does does not tint the water yellow, brown or even green. Anytime the water takes on a distinctly yellow or brown tint, the problem is dissolved organic material rather than bacteria, so you can rule out bacterial blossom as the root cause.
It is wise to remember that there can be multiple issues going on at the same time. So if you have tinted water that is also very cloudy, rather that being clear but tinted, consider the possibility that more than one problem is occurring, and act accordingly.
DOC - Dissolved Organic Compounds
You may have heard someone say tinted or cloudy water is caused by DOC, and wondered what that means. DOC stands for dissolved organic compounds, and simply put is any organic matter that has broken down in the aquarium water. It could be fish waste, uneaten food that has decayed, decaying plant parts or even a dead fish that has decomposed.
All of these sources can result in organic compounds that become dissolved in the water, thus changing the makeup of the water. Can these compounds harm the fish? Yes they ultimately impact the health of your fish, because over time they will contribute to changes in the water chemistry that are harmful to the fish. Dissolved organic compounds also will give rise to unpleasant odors and cause the aquarium to look less attractive.
One cause of brown or yellow water that is usually not a problem is tannin. Tannins are present in driftwood, and over time will leach into the aquarium water, staining it yellow to brown. Tannins have the effect of lowering the pH of the water, as well as softening it. For some fish this may be desirable, and even recommended. This is particularly true of fish from South America that require soft acidic water to thrive, and promote spawning.
The first step is to test the water, and determine the pH, ammonia, nitrite and nitrate. Also examine the tank carefully. Is there a lot of debris in the tank? Dead plants, uneaten food on the substrate, perhaps even a missing fish that might be hidden somewhere and decomposing? Do you have any driftwood in the tank? Is the filter running normally? Does the water have foam on the surface? If you take some water and put it in a closed container and shake it, does it produce foam? All of these will be clues to sorting out the root cause, and resolving the problem, if there is one.
Fixing Yellow/Brown Water
Once you've completed your tests and observations, you can now determine what course of action to take.
Tannins - An acidic pH along with driftwood in the tank, is a strong indicator that tannins have leached from the driftwood. This is not a problem unless you are keeping fish that require a significantly higher pH. If driftwood is the cause, the tinted water will clear over time, as eventually the tannins in the driftwood will be exhausted. In the event you are keeping fish that require an alkaline pH, you should consider changing your aquarium decor to something that will not lower the pH.
Biologicals - If ammonia or nitrite are elevated, the biologicals are not stabilized sufficiently to keep toxins in check. Because both ammonia and nitrite are potentially lethal to fish, you should take steps immediately to lower them.
Organics - If the tank has lots of uneaten food, decayed plants, or possibly a dead fish, it needs some cleanup. Likewise, if the water is foamy, or foams when shaken, there are plenty of dissolved organics in the water. In this case, the best course of action is to clean things up. That means removing all decaying materials, whether that be uneaten food, dead plants, or a fish corpse. Vacuum the gravel and make sure the filter is running at normal output. If the filter is slow, odds are it's clogged with debris, which is another potential source of organics.
It may take some time to clear up the water, but eventually it will be resolved. Continue a regiment of regular maintenance, and the problem is not likely to reoccur.