The methods used to maintain a nano reef can vary greatly throughout the hobby. The methods described below are what I have found to work best in maintaining a successful nano reef. Simplicity is the key in nano reef keeping; inexpensive and easy to follow. This is of course by no means the only way to keep a nano reef. I will try to best explain everything, but should you have any further questions with this, please search existing topics or start a new topic on the forums.
The natural method of filtration consists of only liverock and livesand. No protein skimmers are used and no additives are dosed. The nutrient export is provided by frequent partial water changes of 10-15% about every week. Trace elements are replenished through water changes.
As you go about purchasing all of the supplies for your new nano reef, you're going to have to make a decision on which salt mix you should use. Because no additional dosing is usually done with this method, you will want to be using a good reef salt mix. Not all reef salts are created equal however. Unfortunately there is no set data that clearly shows which salt is better over another, which makes the decision even more difficult. The best recommendation I can make is to search around the online forums and see which ones people like best from their experiences.
When starting out your nano reef, your first livestock purchase will be liverock and livesand. You will want to purchase the highest quality live rock as you can possible afford. It will be the entire basis of your filtration so there should be no skimping. Only a small quantity of liverock is needed, so cost shouldn't be so much of an issue. For information on the different types of liverock, refer to the Liverock Selection article. Placement of your liverock can be nearly anything you like, just keep in mind that the more open it is the better.
In this type of system livesand is also important. You can purchase livesand from a variety of places, or create your own livesand by seeding dead aragonite with some sand from an established system. The depth of sand can vary to anything you like. Sand beds from 1/4"; to 4"; won't produce much of a difference in this system, but there are benefits to both. If the bed is deeper is tends to be a more efficient filter. If you choose to have a deep sand bed, make sure you have plenty of detrivores to keep the sand stirred.
With this natural method, no protein skimmers or dosing is used. Studies of skimmers have shown that they remove various trace elements, along with pods and plankton. When people run protein skimmers, they dose trace elements to replenish them after their corals and skimmers use them. Because the skimmer removes most of the elements, such as iodine, it is dosed back in causing almost an endless cycle. The main problem this holds in nano reefing is that many of the trace elements cannot be easily tested for, so no one ever knows where their level is. This can lead to overdosing which will crash a nano reef in a matter of hours. The skimmer also begins to starve your corals by removing their food source. It's simply too risky.
Protein skimmers are beneficial however, because they remove excess nutrients from the water, but this advantage is out weighed by the disadvantages. To remove the excess nutrients from this system you do a partial water change. The water change also doubles to replenish your trace elements, which are in your synthetic sea salt. Nitrates are removed, dissolved organic compounds are removed, and your trace elements are replaced. Your nitrates will always be at or near zero, and the elements will stay at a consistant level.
The whole maintenance procedure only requires about 15 minutes a week, so everyone can handle it. You can take short cuts to save time by pre-mixing water in a new, never before used, 5 gallon bucket and keeping it circulating at all times. Then when it's time to change your water, just scoop it from there. More details on the water changes can be found in the Maintenance article.
The last key factor to this system is having good flow. Use a powerhead or two to give you a flow rate of about 7-10 times the tank's total water volume.
I encourage everyone to try this method for their nano reef. It is uncommon to not use a protein skimmer, but nano reef keeping isn't the same as a traditional sized reef (though this method still works great on larger tanks). It's simple, it's cheap, and there is no extra equipment to worry about. As I always say, the less 'toys' you have on your reef, the less there is to go wrong.