Even among experts, controversy exists about what constitutes the "best" filter for a live reef aquarium. Still, any list of prudent filters to consider would include live rock, protein skimmers and sump filters, which most serious hobbyists consider essential for marine aquariums in general and reef tanks in particular. These three filter types provide critical filtration.
In aquariums, you have to provide three types of filtration: mechanical, chemical and biological. Mechanical filtration consists of physically straining debris from the water. In chemical filtration, chemical processes serve to remove noxious chemicals from aquarium water. Biological filtration provides long-term stability and encourages beneficial bacteria to grow. These bacteria break down fish wastes like ammonia and nitrite, converting them into less-toxic nitrogen compounds.
Live Rock and Live Sand
Live rocks and live sand provide biological filtration. Live rocks consist of old, dead coral skeletons colonized by other organisms. They include the bacteria that break down fish waste. Live rocks and sand have a favorable surface-area-to-volume ratio, encouraging the bacteria to thrive. Live rocks provide powerful biological filtration, and serve as the framework for the rest of the reef tank. Most corals and other sessile invertebrates can be mounted on live rock.
Protein skimmers straddle the line between physical and chemical filtration. Protein skimmers create tiny bubbles that move up through the body of the protein skimmer. Organic compounds such as free-floating protein particles stick to the surface tension of the bubbles and collect at the top of the skimmer in a fine foam. Several types exist in the aquarium hobby, including the old-style air-stone skimmers and the more advanced venturi skimmers. Air-stone skimmers cost less and are less efficient. Venturi skimmers cost more but are smaller and quieter. Cost and space usually determines which skimmer most people use.
Sump filters consist of a second container of water, often a re-purposed fish tank. Most marine aquarium hobbyists take a DIY route and make their own, customizing the sump to their own needs. Depending on the specifics of your design, a sump filter can provide all three types of filtration. They often include media designed to encourage the growth of beneficial bacteria -- even extra live rocks. Sump filters offer the fringe benefit of letting you hide equipment like protein skimmers in the sump, out of sight in the aquarium stand.