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Hum, Crackle, Knock: Monitoring Reef Habitats in Florida Keys National Marine Sanctuary

By Leila Hatch

Listening to the sounds on a coral reef provides a wealth of information to researchers studying reef ecosystem health over time. In Florida Keys National Marine Sanctuary, listening with underwater microphones (hydrophones) is helping scientists learn about how people use reef areas, as well as how invertebrates, fishes, and marine mammals are using different reef habitats. 

As the only barrier coral reef in North America, and the third-largest in the world, divers and snorkelers flock to Florida Keys National Marine Sanctuary to look beneath the surface of its turquoise waters at the colorful and diverse species that live there. Over the decades in which the sanctuary has been working to protect these iconic reefs, sanctuary researchers and partners have been trained as the eyes underwater – surveying the reef health systematically, and helping managers monitor the status of the corals and the ecological communities that depend on them.

Although an important tool for monitoring, human vision has its limits underwater. For one, light does not travel very far underwater, and is lost quickly with depth. Second, many animals are active at night rather than in the light of day. However, many reef animals make sound and rely on their sense of hearing to detect their predators and prey, to find mates, retain groups, find food, and select prime habitats that will protect them. Listening underwater, therefore, is an important complement to our visual surveys that can fill in information about animal presence and behavior, supporting our ability to monitor reef health over time.

Researchers from many institutions have placed hydrophones, or underwater microphones, in and around sanctuary habitats for many years. In 2016, NOAA began maintaining standardized sound monitoring stations in the sanctuary, an effort that was expanded in 2018 under the Sanctuary Soundscape Monitoring Project (SanctSound), in partnership with the U.S. Navy. Many institutions have been working with NOAA to improve our understanding of what we are hearing in Florida Keys National Marine Sanctuary, and in particular, to design sound measurements that can help us monitor the health of reef habitats.

a map showing the Florida Keys National Marine Sanctuary boundary and location of four passive acoustic monitoring sites.
Locations of the four SanctSound passive acoustic monitoring sites within Florida Keys National Marine Sanctuary (red outline). FK01: Western Dry Rocks; FK02: Eastern Sambo; FK03: 9 Ft. Stake/Eyeglass Bar; FK04: Sombrero Reef. Image: NOAA

Looking for Patterns Across Data Types

To understand which sounds are important to our protective interests on reefs, researchers are comparing sound to other sources of information, including ocean temperature and other water column measurements, diver surveys, images from satellites, tracking information from fish and turtles that have been tagged, and tracking information from vessel operating transmitters.


For example, researchers from North Carolina State University found that low frequency (low pitch) sound levels recorded by hydrophones near established mooring networks maintained by the sanctuary were higher than recordings from areas where mooring is not permitted. They hypothesized that this was due to the heavy use of this area by recreational boaters, especially during the summer months, whose propellers create low pitched sounds that travel long distances underwater.

aerial view of a boat in clear, turquoise water over a coral reef.
Recreational vessels make use of the mooring buoys located at reef sites throughout the sanctuary. Photo: Jack Fishman

To test their hypothesis, they compared sound levels to high resolution satellite images that provide coverage of the Lower Keys region once every few days. Periods like this one, with many boats identified in the image, were found to correspond with louder low frequency sound levels.


Currently, NCSU, NOAA and Florida Fish and Wildlife Conservation Commission are working together to identify many of the animal sounds that we are hearing in the sanctuary. One signal that is ubiquitous in our recordings is one we know well, and it’s made by one of the reef’s smaller inhabitants, the snapping shrimp. If you dive or snorkel in the sanctuary, you have likely heard the crackling sounds made by these little crustaceans. Some say their snaps sound like sizzling bacon. What do you think?

a tan colored shrimp with an enlarged right claw.
Snapping shrimp can be found throughout many habitats in Florida Keys National Marine Sanctuary. Photo: Paul Caiger


We hear lots of fish in the sanctuary. Many fish call during specific times of year and specific times of day as a cue to support mating, or spawning, activity. Sounds produced by black and red grouper are common at some locations within the sanctuary and are being monitored so that we can better understand where and when these important reef predators reproduce. Additionally, as groupers often spawn at locations also used by other fish species, such as snappers, the sounds produced by groupers may help us to identify places and time periods that are important to the life history of many fishes.

A large red fish with a big mouth.
Red grouper represent an important bottom fishery in the Florida Keys. Photo: Greg McFall/NOAA
A large gray and black fish swimming in blue water.
Black grouper are one of the largest species in the Atlantic and live around rocky bottoms and reefs. Photo: Albert Kok

Marine Mammals

Some larger, charismatic inhabitants of the sanctuary, dolphins, contribute their whistles and buzzes to the sanctuary’s underwater soundscape. Dolphins are well-loved inhabitants of Florida Keys waters, and we hear at least two species regularly in the sanctuary: bottlenose dolphins and Atlantic spotted dolphins.

Listening to Mystery Callers

While it is very obvious where some sounds are coming from (e.g., boats and dolphins), for the majority of fish sounds that we hear, we do not know who is making them. Sometimes these sounds are produced so frequently and by so many fish that they create “choruses” in the soundscape. We have heard similar sounds in other places, giving us hints to who might be making them. For example, we hear harmonic “hums” during the spring at night at some locations in the sanctuary. These sounds are strikingly similar to sounds produced by midshipman fish in the Pacific Ocean. We think they are male Atlantic midshipman making sounds to attract females during their spawning season. What do you think?

A fish burrowed in the sand.
Atlantic midshipman prefer sandy or muddy bottom habitats and are nocturnal bottom-feeders. Photo: NOAA Exploration

We hear other fish chorusing around and after dusk in the sanctuary. Some are short bursts of knocking sounds that are repeated as night progresses, while others are higher frequency pulse trains that can persist uninterrupted through the night during the spring season. By comparing our recordings over time with the tracks of specific tagged fish and with periodic underwater surveys conducted by divers, we will keep working to pin down the identity of these mystery callers.

Training Ground for Future Reef Protectors

Our goal in listening underwater in Florida Keys National Marine Sanctuary is to use sound to monitor changes in reef communities over time. Sounds can be collected continuously, through the night, and even through hurricanes (if we’re lucky), all of which is more coverage than we can typically get from other monitoring methods (e.g., scuba diver surveys). More complete monitoring means that we can be more targeted in our protection of fish populations by focusing on the timing of vulnerable activities, such as spawning. We can also understand how reef communities are recovering from coral disease.

The Florida Keys is a special place that inspires future reef protectors. As a doctoral student at North Carolina State University, Kayelyn Simmons has chosen to focus her research on using underwater sounds to assess fish abundance and diversity across different zones in Florida Keys National Marine Sanctuary. Now a John A. Knauss Sea Grant Fellow working for NOAA’s Coral Reef Conservation Program, Simmons says “Just by listening, we know that many areas in the sanctuary are supporting spawning behavior for multiple fish species. Listening to reefs holds great promise for improving the success of our efforts to protect and understand patterns of resilience in these important habitats.”

a person scuba diving and holding hydrophones.
Kayelyn Simmons attaches a hydrophone to the seafloor in Florida Keys National Marine Sanctuary. Photo courtesy of Kayelyn Simmons under FKNMS permit#2016-111A1

Dr. Leila Hatch is a marine ecologist with NOAA’s Office of National Marine Sanctuaries and is the co-lead for the Sanctuary Soundscape Monitoring Project