What is a protein skimmer? A protein skimmer is a device used to remove organic compounds such as food and waste particles from aquarium water. It is most commonly used in commercial applications like municipal water treatment facilities and public aquariums. Smaller protein skimmers are also used for filtration of home saltwater aquariums. ASAP Aquarium offers a fine selection of protein skimmers from JBJ, Reef Octopus and others, to meet the needs of your saltwater and marine reef aquarium.