Unlike most aquarium filters, protein skimmers actually suck waste directly out of aquarium water instead of absorb them or collect them for your manual removal. Skimmers accomplish this by running fine bubbles through a column of water. The surface tension on the bubbles binds to various organic wastes -- protein is only a fraction of the waste -- and bring them to the surface, creating a foul foam. Skimmers can cost quite a bit, but if you are particularly handy, you can certainly build your own.
The main difference between different types of protein skimmers is the different ways they create their bubbles. Venturi skimmers create bubbles by forcing water through a venturi valve, basically a bottleneck. This creates pressure changes that cause bubbles to fall out of solution. These bubbles are tiny, which gives them a favorable surface-area-to-volume ratio. Since they have more surface area per bubble, venturi skimmers are arguably the most efficient protein skimmers. This means that a smaller venturi skimmer can do the same work of a larger air-driven skimmer, making them great space savers. Unfortunately, they are also among the more expensive protein skimmers.
The specifics of building a DIY venturi skimmer will vary greatly based on the size of the aquarium you are trying to build. You will need PVC pipe, fittings and connectors.This is the area where many of the specifics will vary most. You will need one large piece for the main body -- for this piece, clear PVC is ideal -- with connectors to smaller pieces. The main body should be at least 4 inches in diameter, and the smaller pieces should be 2 inches in diameter; but scale it up for larger tanks. You will also need one flat cap for the bottom of the main body, one right-angle connector that can attach the main body to your smaller fittings, and one three-way connector, which can connect the main body to two smaller diameter pipes, one in a straight line and one at a right angle. You will also need food-safe PVC glue and a water pump. You can either get a regular aquarium water pump and a venturi valve or get a venturi pump that already has a venturi pump integrated.
First, you're going to assemble the PVC into a main body tube, which will be upright, with three smaller pipes coming out of it. It should have a flat bottom to rest on. Near the bottom, one pipe will be the output or return line. Near the top, there will be another connection at a right angle, the input. At the very top, in a straight line from the main body, will be another smaller, rigid PVC tube, which will allow the skimmate or foam to leave the skimmer. Connect everything with PVC glue. Use plumber's tape on any connection. Make certain that the input line is plumbed through your pump and/or venturi valve. If it is working correctly, water will move through the pump and valve, in through the input, and slowly through the main body to the output. During this, bubbles from the valve will rise through the water column and create a foam that bubbles out through the waste pipe at the top of the main body.
You have a number of decisions to make before you assemble the skimmer. First, you need to decide if you're connecting the skimmer directly to the aquarium or plumbing it through a sump. For particularly large skimmers, plumbing to the tank might be the only option, though hiding them in a sump is usually more aesthetically pleasing. You will also need to decide if you want to connect the skimmer with PVC plumbing or with vinyl tubing. Vinyl tubing works great for smaller skimmers and lets you see inside the tubing for blockages. But it may not handle the pressure of a larger skimmer. The size is also a consideration. Curiously, protein skimmers are unusual for aquarium equipment in that you want a skimmer to have as slow a flow rate as possible. The longer it take water to move through the skimmer, the more chances the bubbles have to stick to waste products. According to Dr. Frank Marini, writing on the Reefkeeping website, you want a skimmer's turnover to be equal to two times your aquarium volume per day. You can figure this out by calculating the volume of your skimmer and the gallons-per-hour rating of your pump.