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Preparing the Surface
Drain some water from the aquarium. Drain the water low enough to allow room to clean and dry the area around the leak. You can use a cup, bucket, or other container to remove the water. If the leak is at the bottom of the aquarium, you will need to remove all the water and aquarium rocks from the tank. If the leak is very low in the tank, you may have to move the fish and aquatic plants into a temporary container or other aquarium while repairs are made. Keep in mind that the sealant you seal the leak with will have to cure before refilling the tank, so plan accordingly to keep your fish and plants healthy.
Remove the old sealant. Scrape away the old sealant around the leaking area with a razor blade scraper. You want to make sure to remove silicone from the leaking area but you don't want to remove the silicone from between the glass panes. The means that you are just removing the silicone bead on the inside corner of the tank. If you didn't drain the entire aquarium because the leak in high up on the walls of the aquarium, be careful not to allow any of the old sealant to drop in the tank. Silicone sometimes does not bond well with old silicone. You may end up having to remove a lot of the silicone on the inside of the tank and then resealing all the seams at one time. If you are already draining, drying, and scraping silicone, you might as well do the whole thing.
Clean the area. Wipe the area with a clean cloth dampened with acetone. This will remove any residue and other foreign material from the leak area. Dry with a paper towel and allow to completely air dry, which usually takes about 15 minutes. Having a clean area will assure that the new silicone that you apply will hold to the glass and you will not end up with another leak in the near future.
Sealing the Leak
Apply nontoxic 100% silicone sealant to the leak area. Run a bead of silicone along the leak area using a caulking gun. Then smooth that bead out, with a damp finger or a caulking tool, so that the silicone is smoothed out and it completely covers the seam that leaked. Check with a professional aquarium supply for recommended repair products. Make sure that if you use silicone, it is labeled "nontoxic" and "100% silicone". Also make sure that the silicone sealant has NO fungicide in it and is a High Modulus product. You may be tempted to try and repair the leak from the outside of the tank, but usually the repair is more effective if made on the inside. A repair on the inside will hold better, since water pressure will "tighten" the seal pressing the silicone against the glass. If it is applied on the outside, the water pushes the silicone away from the glass.
Allow the sealant to dry. Silicone needs to dry and cure for a minimum of 24 hours. If you are applying it in a cool and dry environment, you may need to wait closer to 48 hours. This time will allow it to set completely, assuring that it attaches properly to the glass and does not leak. You may use a heat lamp or other portable heat source to help cure the sealant, but do not heat above 110 degrees (F).
Inspect for leaks. Refill the tank enough so that there is some water in contact with the repaired seam. Wait a few hours and then fill the tank even further and then look for leaks. Finally, fill the tank all the way and then look for leaks. Take a close look at the area that was leaking and wait awhile to make sure that the water pressure inside the tank doesn't reopen the leak. Try taping a paper towel to the outside of the tank where the leak was and leaving it there for an hour or so. If the towel remains dry, your leak is fixed. Keep towels and a bucket nearby, in case of continued leaking. This will allow you to quickly remove the water from the aquarium once again.
Set the tank back up. If you have removed everything from the tank, including gravel, fish, and plants, you will need to replace them when you are confident the leak is repaired. Begin with the gravel and then add other objects on the aquarium floor. Add any chemicals to the water that are needed and then return any plants and fish back into the tank. This is a really good time to make sure everything you put back in the tank is thoroughly cleaned before you put them back.
Locating Hard-To-Find Leaks
Pay attention to the water level in your aquarium. In some cases, you will first spot a leak in your aquarium by noticing that the water level is dropping. While there is always some evaporation in fish tanks, any noticeable level drop could be due to a leak. If you have a severe leak, the location will likely be very evident and you will be able to find the source from a quick glance around the tank.
Look around the aquarium for wetness. If the leak is not obvious, you may first suspect one if there is unexplained water around the outside of your tank. Even a small amount of unexplained dampness could signal a problem. If you have changed a filter, added items into your tank, or otherwise interacted with the tank recently, water outside of the aquarium may be due to your activities. Try drying it up and then keeping an eye out for additional water pooling up. If the water returns, then you have a leak.
Inspect the tank for the leak location. If you suspect there is a leak, but its location is not evident, then you will need to do a bit of investigating. Look for metal corners that appear to be separated from the glass, and for sealant protruding in the corners. These are tell tale signs that the aquarium has a problem. Also, feel around the edges. If you feel water, move upward from that location, until the surface feels dry. The furthest spot towards the top of the tank that is wet is likely to be the leaking area.
Mark the location of the leak. If you find the location of the leak, or you have an area where you suspect the leak is, you should mark that area with a felt tip pen. This will allow you to keep track of the area once your tank is empty and you begin repairs. Most felt tip pen marks can be easily removed with glass cleaner after you finish your repairs.
Know what leaks cannot be repaired at home. Leaks along the seams of your aquarium are relatively easy to fix because they are usually caused by a failure in the silicone, and silicone can be easily replaced. However, if the leak is due to a cracked side or bottom of your tank, that is not as easy to repair. Replacing a whole piece of glass will take a lot more time, expertise, and energy. Basically, replacing a glass panel of an aquarium will likely require the skills of a professional. If one of the sides or the bottom of your tank has cracked, it is likely that the whole aquarium will fail. A crack in the glass will spread due to the pressure of the water and once it spreads far enough, the glass panel will collapse. Sometimes it's better (and easier) to just replace a leaking aquarium instead of trying to fix it.
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