Fish live in a semi-closed environment. A fish needs to breathe oxygen from the water it lives in. If that water is not kept clean and aerated, the fish will experience a great deal of stress, and stress, in turn suppresses the immune system and makes them more vulnerable to disease and premature death. They are unique pets because they live in an aqueous environment, so if they don't get fresh water, it's like they are living and breathing in the water from their own toilets.
In Nature, most of the fish we have as pets now came from fast-flowing river environments where there is a constant influx of fresh water from mountain resources to wash away wastes and toxic compounds that can accumulate. They unfortunately don't have this advantage in the tank, but a filter is a piece of equipment that can help keep a tank system stay balanced and keep toxic wastes at a minimum.
Most filters work mainly by mechanical and biological means. Mechanically, filters have media like floss to sieve out macroscopic waste products that we can see, trapping particles of dirt, detritus, fish poop, uneaten food, etc.
However, surprise! This is not the major function of a filter at all. It's not these macroscopic particles that really hurt fish; it's more frequently the chemicals in the water that we can't see that hurt them the most. It's these things that can cross gill membranes and interfere with their respiration and day-to-day function.
Here is where the biological function of the filter comes in. Waste products decay into ammonia, and ammonia is a highly toxic substance to fish; it can in fact kill them relatively quickly, or cause them to go into shock (panting, hyperventilating, swimming erratically, laying in the sand, etc.). A established filter that has been running for a long time will have a good population of beneficial bacteria that denitrify ammonia. The process goes from the most toxic forms to the least toxic forms:
Ammonia ==> Nitrite ==> Nitrate (==>Free Nitrogen, rarely in FW tanks, but can happen in a SW reef tank)
Biological filters work by:
1)Providing a ton of surface area for these bacteria to grow
2)Providing constant current, so that the aerobic bacteria get the high oxygen they need
Only an established tank will have bacteria that can convert these toxic compounds. This is the reason why you should cycle your tank before you even get fish with pure ammonia, by the fishless cycling methods linked on the right. This takes patience, but will result in a lot less death and "new tank syndrome" when you do get your first fish, and they will stress and suffer far less.
It does also help to use old filter floss from another established tank in a new filter, as this can help "kick start" the cycling process.
If you do not run more than one tank, you can ask a friend with a healthy tank, or an LFS (local fish store) with a healthy tank (don't go for their sale tanks, use only material from their show tanks which is disease-free) to donate some used filter media. Alternatively, a cup of gravel from an older tank will also help the cycle.
Whatever you do, do NOT stock your tank almost overnight full of a full load of fish, and just expect them to do fine. This will almost certainly result in overwhelming the filter's capacity, because not enough bacteria have had a chance to build there yet to support the life you want to keep in the tank. This will usually result in instant death for a large number of fish at once from ammonia poisoning.
In the end, please note that FILTERS ARE NOT REPLACEMENTS FOR WATER CHANGES. As you can see in the above graph, ammonia and nitrites are reduced, but nitrates continue to rise, and though these are the least harmful of the nitrogenous waste products, high quantities of it are still a stressor. I recommend water changes of 20-30% every 2 weeks or so, even if you have a filter that is running well. As stated above, it's the things that you can't see that are sometimes the most harmful to fish, and a regular water change schedule, along with monitoring ammonia and nitrate levels with a kit, will help insure the long term health of your pets.
The next article in this series, Choosing a Filter Part II, will explain the pros and cons of various filter types.