The Nitrogen Cycle
One day you wake up and notice your aquarium is kinda cloudy..."sigh"...no problem. Most likely its just a few things that you might be doing which are reversible. But lets backtrack a bit and figure out WHY this happens before we get to how to fix it.
Bacteria
When you first start off with a brand new aquarium it is essentially sterile. You start off with a clean empty aquarium, maybe some gravel that you rinsed and some other new or used odds and ends like heaters or pumps. The water in itself is "clean" as in it hasn't been cycled or has any beneficial bacteria that has started the process of helping in the cleaning process of your fish waste and other organic material.
This is where the cycling process begins. The process is basically the same for a freshwater and a saltwater aquarium even though the types of bacteria are different strains for both. There are different ways to begin this process. One of the most common is to fill your aquarium with water and have it function as if it had fish. Have the lights turn on and off, pump runs like normal and in a few weeks time you will begin to see some algae growing and the process of your aquarium's ability to sustain life. This is where the first step of bacteria comes into play. Ammonia will be begin to appear and once the level of bacteria reaches a certain population your Ammonia level begins to drop but until then Ammonia is very toxic to your fish and other inhabitants. Then comes the next step. Nitrites, which is the second step in your cycle. These Nitrite levels are also toxic but will begin to be converted to the less harmful Nitrates by your nitrifying bacteria. These Nitrates can now be removed through you regular maintenance routine of water changes and depending on whether you have a fresh or saltwater aquarium some of the inhabitants can use Nitrates such as live plants in a freshwater aquarium.
So now that we have covered bacteria and its role in your aquarium lets move on to why you might wake up to cloudy water. This cloudy water is actually called a "Bacterial Bloom" it usually happens when your parameters are a little off..or alot off. Say for example you feed too much, or you leave a dead fish in for too long or you just don't clean your aquarium regularly. Initially your bacteria would help in the decomposing of left over food at the bottom of your tank but now you have approached a limit that it cannot adequately break down the food faster than your introducing it to your aquarium. As a reaction your bacteria
kicks into high gear and reproduces very quickly. Resulting in a milky white appearance in your water. No matter how many times you clean your filter it will not remove this because it is much too small to be filtered out by usual mechanical filtration such as canister filters.
This can only be done by doing regular water changes and limiting the food or type of food into your aquarium for awhile as well as maybe removing any decomposing organic material. Overcrowding is also a factor since this will increase the fish waste or "biomass" that is in your aquarium. Imagine having 50 people in your living room. The amount of waste that will be produced is much greater than 10 people. So you always have to know how much waste your aquarium filter can handle as well as maintaining proper aquarium husbandry. In time you will see that your water will become more and more clear as the extra bacteria will now die off since there is not enough food to sustain it and your bacteria levels will reach an equilibrium.
Just remember...
Don't overfeed
Perform regular water changes
Do not overcrowd your aquarium
Remove excess organic material as soon as possible (Dead fish, food,dead or dying plants or coral)
It is your responsibility to look after these creatures just as you look after any other pet. They are dependent on us to give them a healthy environment to live in.