Slugz here are the most common methods of filtration... I got all of this information from
http://www.masla.com
A freind that builds tanks recommended the masla site awhile back and I pass it along whenever I can. I hope it helps
The Standard method.
Water exits the tank via an overflow system at the the top of the tank. It then passes through a pre-filter pad that traps out the large particles of debri and is plumbed downwards to the wet-dry filter.
The standard wet-dry filter utilizes bio-media, such as bio-balls, within the filter. The idea of the bio-balls is they offer a tremendous amount surface area for bacterias to adhere to, as well as, allow air ( oxygen ) down into the media. The increased amount of oxygen being exposed to, in combination with the thin sheets of organic laden water passing over, the bacterias allows for a far more effective bacteria. Keep in mind that is the amount of oxygen that allows the bacteria to oxidize waste. The wet-dry filter is extremely effective in converting ammonias ( NH4 ) and ntitrites ( NO2 ) into the lesser toxic form of nitrate ( NO3 ).
Aiding the filtration process is a protien skimmer or foam fractionator. Essentially a protien skimmer helps remove compounds from the water using heavy aeration to drive organics out of the water thus lessening what the bacterias need to deal with.
Within the tank, at the bottom, is a layer of sand or gravel approximately 1" deep. This represents the ocean floor. Placed upon the sand bottom is the live rock. The live rock forms the foundation that the living corals are placed upon.
The Berlin method
Supposedly based upon reef tank filtration used in Germany, this method decreases the effectiveness of biological filtration by relying solely on the bacterial populations contained on and within the live rock. There is no pre-filter pad within the overflow system and all the bio-balls in the wet-dry filter are removed. The wet-dry filter simply becomes the 'sump' or reservoir below the aquarium.
The thinking is that the prefilter pad and the wet-dry filter are too efficient. The pre-filter pad eventually becomes biologically active as it traps its debris and ultimately aids in converting wastes. The bio-balls, in combination with the increased exposure to air ( oxygen ) too effectively convert ammonias ( NH4 ) and ntitrites ( NO2 ) into the lesser toxic form of nitrate ( NO3 ). Both the pad and the bio-balls ultimately produce Nitrate, which in standard method leads to quicker and higher levels.
A greater emphasis is placed on the protien skimmer. Since the protien skimmer helps remove compounds from the water it lessens what the bacterias on the live rock need to deal with.
Within the tank, at the bottom, is NO sand or gravel. A bare-bottom tank harbors less biological activity, and is much easier to remove the debris that will settle there. Again a decrease in biological filtration produces a slower developement of Nitrate. The live rock, the foundation that the living corals are placed upon, is placed directly on the bottom of the tank.
The live rock by itself contains a tremenous amount of bacterias, and due to the lower amount of oxygen available to them they do NOT convert wastes as effectively. The end result is a very capable filter system, and one that does not generate Nitrates as quickly.
NOTE ; partially in lue of the sand at the bottom of the tank, which helps produce calcium, the Berlin method uses heavy amounts of Kalkwasser ( calcerous water ) for evaporative replacement.
The Algae Scrubber method
As opposed to a wet-dry filter Algal Turf Scrubbers grow ( turf ) algaes on screens that are in a seperate, but connected, system located outside or below the main aquarium. The basic concept is that the algaes remove nutrients from the water as their food source.
These screens should be scraped every 4-7 days as the algaes grow most rapidly when they are short. Harvesting the algaes regularly during their peak growth phase allows the nutrients, which are drawn up inside the algae, to be removed from the entire system.
The flow of the water across the screen(s) comes from the main tank and is returned to the tank That flow should be regulated, and if possible, alternated not just run from one end of the system to the other. This can be accomplished by a tilt tray or a dump bucket that creates a surge across the trays. The surge idea is to give the algae time to exchange gasses and absorb nutrients as well as provide light to all sides of the algae for maximum growth in a small area.
For these algaes to grow they need light. The lighting of an algae scrubber should be run the opposite to when the main tank lights are on. The reason for using a light cycle opposite from the main tank is to maintain stable pH, oxygen and carbon dioxide levels within in the system due to photosynthetic respiration. This prevents the wide range fluctuations found in most tanks. The type and output of the lighting will also affect the type of algae and growth rates. Nearly any type of intense light can be used, metal halide, VHO and HO flourescents, mercury vapor, halogen to name a few.
Within the tank, at the bottom, is a layer of sand or gravel approximately 1" deep. Placed upon the sand bottom is the live rock. The live rock forms the foundation that the living corals are placed upon.
The Jaubert method
The Jaubert method does NOT use an overflow nor does it have a reservior below the aquarium. Dr. Jaubert, of the Monaco Aquarium, promotes a variation of the Lee Chin Eng system which uses the 'natural' approach. The main variation is the introduction of a Plenum at the bottom of the tank.
A plenum is a gap or void space underneath the one to four inches of live sand at the bottom of the tank. Typically this void space is 1 inch deep and this area becomes anoxic, or an area low in oxygen. This anoxic area creates a 'ying-yang' enviroment where oxygen strarved organisms breakdown or remove components from the oxygen carrying organisms and components. The natural reduction of Nitrate ( NO3 ) in these systems is the direct result of a plenum as it generates a 'de-nitrification' process that robs the nitrate complex of its oxygen. Another benifit of the two opposing enviroments is the natural dissolution of calcium, magnesium, and strontium to natural levels within the aquarium.
The Jaubert system does not use a protien skimmer as the removal of organics via skimmer would decrease the effectiveness of the plenum. Additionally the only water movement within the tank is that of an airstone and its resulting rising bubbles.
Placed upon the sand bottom is the live rock. The live rock should be strategically positioned so that minimizes the amount of sand that it actually covers, as the covered spots would quickly cause dead areas within the sand that it sits upon.
The Live Sand Bed method
In a reef tank with a live sand bed ( set up properly ) the hobbyist is creating an enviroment that is more 'ecologically complete' or dynamic, certainly more like a true reef enviroment. As debri from the tank settle at the bottom of the tank there are a number of animals that feed on that debri, lets call them detrivores ( animals whose food source is the debri of other animals). These animals consist of crabs, shrimps, snails, starfish, sea cucumbers, and bottom-dwelling fish. Whether or not these animals actually consume or simply break up the debri into smaller particles, they are making that debri even smaller and easier for the next level of organisms to break it down further, physically and chemically.
The next level of 'micro-fauna' are the worms, bugs, and micro-scopic forms of life. These creatures help to break down the debri even further, but their greatest benifit is keeping the sand loose, or moving, and this allows oxygenated water to penetrate the sand bed. If one were to place a non-living bed of sand in a tank eventually it would become oxygen depleted. The results of this no-oxygen ( called anoxic or anaerobic, meaning low or without oxygen ) enviroment would be hyrodrogen sulfate ( that rotten egg smell ), and the bed would eventually 'clump' together and become solid. The worms, bugs, and micro-scopic life within the sand keep it loosely suspended which allows oxygen down into the sand thus assisting the aerobic ( meaning with oxygen ) bacteria in being able to continue to chemically convert the debri, biologically speaking.
There are many proponents of live sand beds. Their general consensis is that this bed of sand should be three to four inches deep, at the least. Some actually promote sand beds as deep as ten to twelve inches.
Placed upon the sand bottom is the live rock. The live rock forms the foundation that the living corals are placed upon. The overall benifit of live sand beds is a more complete 'ecologically' balanced system. Additionally, the processes of these small forms of life keeping the sand bed moving, is the breaking down of the substrate itself, thus various trace elements and calcium are released naturally back into the water.
The Mud / Eco method
If one were to take the basic concepts of all the methods above you would have the Mud System.
Envision removing all the bio-media from the sump below, place a layer of 'mud' across its bottom, illuminate this chamber with light and grow various algaes within it, you would have the Mud System. Granted that is the simplified version, so let me explain.
The layer of 'mud' becomes a low oxygen enviroment allowing various anoxic bacteria's to perform de-nitrification. The algaes harbor many small creatures who help break down the debris, and in combination with the debris this enviroment creates a fertile area for the plants to grow. The plants, via photosythesis, consume a large percentage of the nirtogen rich debris. The illumination, which is the opposite time frame of the main tank, provide the energy for the plants, as well as, minimize the pH and carbon dioxide fluctuations within the aquarium.
Within the tank, at the bottom, is a layer of sand. Placed upon the sand bottom is the live rock. The live rock forms the foundation that the living corals are placed upon
. Now, did your LFS (local fish shop) suggest the fluval or undergravel? Don't listen to them. Here's the problem with a U/G, canister, or W/D. They all produce loads of nitrate, which when your keeping reef corals, is your absolute enemy (of many). 
