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Preparation
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Prepare your equipment before you start. Remove any fish from your main tank and put them in a safe place. Drain the main tank so that you're working with a safe, dry environment. Remove your pump and filter, along with all their wiring and rinse them off. Clean the tank or box you're going to be using as your refugium by rinsing it with clear water. Decide on your setup before you start; for an under-tank refugium, it will be most convenient to have your aquarium on a shelf system. It's best to decide on the setup now, before you fill the system with water.
Gather the tools you need before you start. For this project, you'll need a power drill, sealant, a twist valve and two pieces of plastic hosing. The plastic hosing should be able to reach from the top of the main tank to the bottom of the refugium without kinking or being pulled out of the water. Buy this hosing at your local pet or fish supply store.
Set Up
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Drill two holes in the back side of the main tank. Drilling the holes near the bottom will increase the work of the filter, as sediment tends to settle to the bottom of a tank. Doing so will also keep your fish tank cleaner. These holes should be slightly larger than the diameter of the plastic hose you're using; the hose should be able to fit snugly into the holes. Fit the plastic hoses into the holes, with the end extending into the fish tank by a couple of millimeters. Use the sealant around the outside of these connections, to secure the hoses and seal the holes.
Attach the other ends of the hoses to the pump and filtration system, which will now be housed in your refugium. Attach one hose to the sucking valve of your system, for sucking water out of the main tank and into the refugium. Attach the other hose to the pumping valve, to pump water back up into the main tank. Your filter will filter water from within the refugium, while your pump will be responsible for maintaining the water circulation between the two tanks.
Put a squeeze valve on the hose, next to the pumping function. You will use this valve to control the flow of water from the refugium into the main tank, as it's important that both water levels stay consistent. Place the pump and filter system in your refugium, but do not turn them back on.
Finish
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Fill your main tank and refugium with water and turn your pump and filter back on. Turning the pump and filter system on dry will cause them to burn out and be destroyed. Once both tanks are full and your system is running, monitor the cycle for at least half an hour to watch the water level. Adjust the pump as necessary so that the refugium doesn't fill too quickly and overflow, or run dry.
Allow your system to run for an hour to clean out dust or debris introduced during construction. Check the hoses at the back of the main tank to make sure they're not leaking. Once you have trouble shot your system, put your fish back into the main tank.
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Step-by-Step of Setting Up an Under Tank Refugium
Refugiums are secondary tanks that act as "extras" for a fish tank. Although they are separate tanks or boxes, they share a water supply with the main aquarium via the pump and filter and add additional water capacity to an existing setup. Refugiums, also called sumps, are used for a variety of purposes: to house and hide filtration and pump equipment, to grow food organisms such as krill, to increase water capacity and to provide a "refuge" for young or small creatures. They are relatively simple to set up with the right equipment.