If fish relied solely on constant swimming to maintain their current water depth, they would waste a lot of energy. Many fish instead rely on their swim bladder, a dorsally located gas-filled organ, to control their stability and buoyancy in the water column. The swim bladder also functions as a resonating chamber that can produce and receive sound, a quality that comes in handy for scientists locating fish with sonar technology.

Scientific divers can make direct visual observations to support what we know about the underwater world and build an understanding of marine habitats and their inhabitants. But these observations don’t tell us everything, so we supplement them with other tools, like sonar, to provide a rapid survey of a large area in a non-destructive and minimally invasive manner.

Fisheries sonar works by emitting pulses of sound and measuring the return strength. Anything having a different density from the surrounding water (e.g., fish, plankton, air bubbles, the seafloor) can return a signal. In fish, the resonant swim bladder provides the greatest contrast from the water, and the larger the fish, the greater the strength of the returning echo.

The real advantage of fisheries sonar is that it captures a "virtual reality" of how fish use coral reef ecosystems. When that information is combined with GIS and other visual software tools, scientists can "reconstruct" the ecosystem. NOAA scientists create three-dimensional maps from sonar data to figure out where fish are hanging out, what types of terrain they like, and possibly where they spawn.

Tropical island communities rely on healthy reef fish populations for recreational and commercial fishing and tourism, and understanding where and why these fish congregate helps managers address coral reef conservation needs. Fisheries sonar, in combination with seafloor mapping, serves to reveal the preferred environmental conditions at fish "hot spots."