Because sponges contain a variety of chemicals that affect living organisms (bioactive compounds), they have become the subject of research to find drugs to treat human diseases. Haplosclerida sponges have been especially fruitful for bioactive compounds. The upwards of 30 compounds called 3-APs found in haplosclerids have properties such as keeping bacteria from growing and stopping cells from dividing. Not only might they be valuable for human medicines, but they also help the sponge stay healthy. A greasy coating of 3-AP compounds on the surface of a haplosclerid sponge is like a repellant for bacteria and other organisms that could contaminate it. The trick for our using these compounds is how to get large enough amounts without hurting wild populations of sponges. Scientists are working to synthesize (make copies of) compounds like the 3-APs rather than take them directly from sponges.

Sponges host many organisms living on their surface or even inside them. They make great homes because they do not move much, may live a long time (some for hundreds of years), and have hollow bodies with lots of cavities and canals. A single sponge might provide a condominium for organisms as tiny as bacteria and as large as sea stars. The nature of the relationship between the host sponge and its occupants varies. A "parasitic" occupant, such as a mite that lays eggs inside a freshwater sponge, harms the sponge. In many cases, though, a sponge has commensal occupants, who benefit from living there but do not hurt the sponge. The sponge may even have a "mutualistic" relationship, such as with shrimp that keep it clean by living in its canals and eating debris or with bacteria that make toxic chemicals that repel sponge predators. In any case, a sponge is rarely alone.