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New Rocks
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According to "Goldfish," rocks should never be taken from the wild for aquariums. They may be coated with pesticides and other harmful chemicals that cannot be removed and will quickly poison the fish. Rocks should be taken from healthy fish tanks or should be bought from aquarium supply stores. Even then, they need to be scrubbed with hot water, but no soap or cleaner of any kind. The scrubber should only be used for aquarium ornaments and should not clean anything else, lest it pick up chemicals which can kill the fish. They should also be soaked overnight in a new bucket of tap water with a teaspoon of salt added. The bucket should only be used for working with the aquarium.
Regular Maintenance
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Rocks need to be cleaned to remove uneaten food, fish waste or algae growth. "Tropical Fishlopedia" recommends using a soft, bristled algae scraper for use even on the aquarium glass. One slip with a metal algae scraper, and it may crack the glass. The scraper should only be used for that aquarium and should clean nothing else to save on contamination. Rocks can be taken out of the aquarium and scrubbed in a sink. Because of how wet the rock will be, scrubbing it will splash a lot of water around, so be prepared. If the detritus can be easily brushed off, do so before a water change and siphon the waste away.
Extreme Circumstances
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If there was a problem with a parasite or a disease in the tank where all of the fish were killed off, the bacteria in the tank may not be so friendly. Then you will have to clean out everything inside of the tank, including the rocks. Soaking the rocks in boiling water and leaving them out to dry for a week should kill off all bacteria on the rocks and other ornaments. If the rock is porous, however, throw it out and get another rock. It can be difficult to completely sterilize a porous rock.
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Cleaning Fish Tank Rocks
Popular kinds of rocks for aquariums include slate, granite and sandstone. No matter what rock you choose for the aquarium, it will eventually become covered with algae. If you are using live rock for your salt water aquarium, do not clean it. That rock is coated with friendly bacteria that helps keep the water chemistry of the tank balanced. The fish or invertebrates in the tanks will eat off the any algae growths.