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National Estuarine Research Reserves (NERRs)

Rookery Bay National Estuarine Research Reserve

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Rookery Bay National Estuarine Research Reserve is comprised of 110,000 acres of land and water and encompasses 40% of Collier County’s coastline. It begins just south of the City of Naples at Gordon’s Pass and includes Keewaydin Island and the Ten Thousand Islands. The Reserve borders Everglades National Park on the east.

HISTORY

In the 1960s, with farms, buildings, roads and canals springing up across coastal Collier County, residents started to take notice that the once pristine bays and estuaries were showing the effects of development upstream. The Collier County Conservancy, the National Audubon Society and the Nature Conservancy galvanized community support that resulted in more than $600,000 being raised to buy and protect 3,362 acres of land.  This land ultimately became the Rookery Bay Sanctuary.

Throughout the 1970s, the community continued to buy land with funding from community fundraising efforts and philanthropic donations to the cause, eventually completely enclosing Rookery Bay. The Conservancy also continuously worked to exchange 13,000 acres of land from the Deltona Corporation. Their efforts were eventually successful, bringing the reserve to its present-day acreage. In 1977, work was completed for Rookery Bay to be declared a National Estuarine Research Reserve.

PUBLIC ENGAGEMENT OPPORTUNITIES

Volunteer Opportunities

Team OCEAN is a group of dedicated volunteers focused on outreach and education for boaters, beachgoers and people fishing in Rookery Bay AP waters. They educate visitors about the importance of not disturbing nesting birds and retrieving fishing lines to prevent bird entanglement. Their boat-based activities allow them to interact with people across the Reserve, especially on barrier islands where endangered birds nest.

Volunteers also assist with water quality monitoring, fisheries research, sea turtle nest monitoring and shorebird monitoring. Beach and mangrove cleanups are conducted throughout the year, often involving school groups and local organizations. Hundreds of volunteers contribute over 18,000 hours annually to the preservation and management of Rookery Bay AP, participating in various roles such as aquarium assistance, education and special events. 

To become a volunteer, please fill out a volunteer form and join us for a volunteer orientation.

Internship Opportunities

Rookery Bay NERR is also a place to educate and mentor the next generation of environmental scientists and biologists through robust internship opportunities available year-round. Students from all over the world come to learn from Rookery Bay’s team of biologists, scientists and educators with hands-on experiences in the reserve’s 110,000 acres. Opportunities include both college level internship and graduate fellowships, including the Friends of Rookery Bay’s Sea Turtle monitoring summer internship, Minority in Science shark science internship, the Laverne Gaynor scholarship in science and education, NOAA’s Holling Scholar internship program and the Margaret A. Davidson Fellowship.

Events

Special events and educational programs include a yearly lunch & learn series, art reception nights, Festival of Birds field trips into nature, Rookery Bay Community Day, Marine Science Camp, Wildlife and Watercolors Class, Birding with Biologists class, Photography Class, Forest Bathing and much more. The Friends of Rookery Bay offers guided-eco tours to get out on the water by boat and kayak. A variety of adventures are offered including Essence of the Estuary in the Back Bays, Barrier Island Shelling, Ancient Island Excursion, Sunset Bird Rookery Cruise and Sunset Beach Cruise. An ADA accessible boat is available as well.

Educational Opportunities

Rookery Bay NERR offers educational opportunities for adults and students. Rookery Bay partners with the Collier County Public School System for educational fields trips for students in grades 3-12. Students learn about the water, fish and research happening at Rookery Bay. Activities include seining with nets for marine critters, examining plankton under microscopes, taking boat rides with a partnering organization to see wildlife, visiting barrier island beaches and conducting boat trawling.

Community members can explore the Reserve through boat and kayak eco tours offered by the Friends of Rookery Bay. Adventures include Essence of the Estuary in the Back Bays, Barrier Island Shelling, Ancient Island Excursion, Sunset Bird Rookery Cruise and Sunset Beach Cruise. An ADA accessible boat is available.

The Rookery Bay Environmental Learning Center features marine life exhibits designed to mimic the Reserve's natural environment, with detailed rock formations and local marine life. Docent-led programs are available throughout the day.

The “Estuary Encounter” touch tank houses more than a dozen species of marine animals. Visitors can hold a sea star, spider crab or lightning whelk. Upstairs, the Environmental Learning Center’s showcases 3,000 years of human use in the estuary. A large topographic map on the wall depicts prehistoric and historic sites, a storytelling booth recounts memories of pioneer settlers and a tribute to the Children’s Column on Henderson Creek tells how Rookery Bay was saved from development in the 1960s.

SCIENTIFIC INFORMATION

Rookery Bay National Estuarine Research Reserve contains numerous prehistoric shell mound sites, predominantly on mangrove-forested islands and within coastal scrub and pine flatwood habitats. These sites, dating back approximately 4,000 years to the Late Archaic period, offer a glimpse into the lives of early inhabitants, including the Muspa and Calusa peoples. Archaeological investigations have revealed artifacts like shell tools, pottery and remnants of settlements, suggesting the presence of complex communities.

In the early 1880s, the Little Marco Settlement was established between Naples and Marco Island, shortly after the Homestead Act began encouraging Americans to spread out across the country. People primarily made a living off the richness of the estuary — catching fish, harvesting shellfish and growing small plots of winter vegetables. These islanders laid their loved ones to rest in a central location on high ground on the mainland near what is now Shell Island Road. Modest shell tabby slabs identify some of the older graves, with the earliest marked graves dating back to 1888.

Rookery Bay National Estuarine Research Reserve is situated on Southwest Florida’s Gulf Coast. It exhibits a diverse geological history influenced by fluctuating sea levels and the underlying Tamiami Formation. This formation, dating back to the late Miocene to Pliocene, forms the bedrock of the region. During the Pleistocene era, sea levels repeatedly rose and fell, leaving behind remnants of ancient shorelines known as terraces. Two prominent terraces in Collier County, the Talbot and Pamlico, provide evidence of these past sea level stands. The Talbot terrace, formed when sea levels were significantly higher, is evident in the higher elevations of the county. The Pamlico terrace, formed at a slightly lower sea level, also contributes to the county's unique topography. These terraces, along with the Tamiami Formation, shape the landforms and habitats found within Rookery Bay Aquatic Preserve.

Rookery Bay National Estuarine Research Reserve boasts a thriving ecosystem characterized by a mosaic of habitats including one of the only pristine mangrove forest estuaries in the United States. Rookery Bay NERR’s interconnected habitats of uplands and water support an abundance of wildlife, including over 150 species of birds and numerous threatened and endangered animals. The reserve’s mangrove coastlines play a vital role in maintaining water quality, acting as natural filters and providing nursery grounds for fish and shellfish. In addition, Rookery Bay NERR’s mangrove forests help stabilize the coastline, reducing erosion from storm surges, currents, waves and tides. It protects the coastal community by acting as a natural buffer between land and water during intense storms and hurricanes.   

Uplands, comprised of hammock and scrub, contribute to the ecosystem's diversity by offering shelter and foraging opportunities for terrestrial wildlife. This complex interplay of habitats underscores the importance of Rookery Bay NERR in safeguarding the biodiversity and ecological integrity of Florida's southwest coast.

Nesting and Migrating Birds
American kestrel, osprey, bald eagle, turkey vulture, black vulture, short-tailed hawk, peregrine falcon, merlin, Cooper’s hawk, swallow-tailed kite, red-shouldered hawk, anhinga, double-crested cormorant, great blue heron, great egret, white ibis, little blue heron, tricolored heron, yellow-crowned night heron, wood stork, roseate spoonbill, brown pelican, American white pelican, green heron, laughing gull, least tern, American oystercatcher, sanderling, black skimmer, royal tern, magnificent frigatebird, mangrove cuckoo and belted Kingfisher.

Mammals
Black bear, bobcat, bottlenose dolphin, eastern cottontail rabbit, Florida panther, West Indian manatee, river otter, wild pigs (invasive) and white-tailed deer.

Reptiles
American alligator, American crocodile, southern black racer, cane toad (invasive), diamondback terrapin, eastern diamondback rattlesnake, yellow rat snake, Burmese python, eastern indigo snake, Florida box turtle, Florida softshell turtle, gopher tortoise, green anole, green iguana (non-native/invasive), green tree frog, mangrove water snake, loggerhead sea turtle, green sea turtle, Kemp’s ridley sea turtle.

Fish
Atlantic spadefish, barbfish, bighead sea robin, black drum, code goby, crested goby, gambusia, giant rays, goliath grouper, goldspotted killifish, Gulf flounder, hardhead catfish, inshore lizardfish, lane snapper, lined seahorse, lionfish, lookdown, orange filefish, pipefish, polka-dot batfish, pygmy sea bass, spotfin jawfish, sharks, smalltooth sawfish, smooth butterfly ray, snook, southern stargazer, southern puffer and striped burrfish.

Shells and Mollusks
Banded tulip, fighting conch, horse conch and oysters.

Crustaceans
Blue crab, calico crab, common snapping shrimp, ghost crab, giant hermit crab, mantis shrimp and spider crab.

Other Invertebrates
Brown spiny sea star, horseshoe crab, moon jelly, nine-armed sea star, pygmy sea cucumber, sand dollar, tri-colored anemone, upside-down jelly and variegated sea urchin.

A full list of species can be found in the Rookery Bay NERR Management Plan.

Conservation Efforts

Rookery Bay Research Reserve is here to protect 110,000 acres of land and water in Collier County for future generations to enjoy and experience. Rookery Bay Research Reserve protects and conserves land, water and wildlife through research, education, conservation and coastal training for decision makers, community members and local professionals. 
 
Through research, Rookery Bay is leading the way for innovative conservation and land management practices — crucial for adapting to constantly changing environments. By monitoring the water, weather, plants and animals, Rookery Bay Research Reserve is helping scientists and government leaders detect differences before they become problems.

Rookery Bay’s education program is inspiring area students and teachers to be stewards of the coast as well as educating over 50,000 adults each year through visits to the Environmental Learning Center eco-tours, classes, events and outreach programs.

Every summer, conservation staff members work to protect hundreds of sea turtle nests from predators, giving thousands of hatchlings a chance to reach the sea. Staff members also work on land to eradicate non-native, invasive plants and animals threatening Florida’s beautiful native wildlife — none more challenging than Burmese pythons. Rookery Bay Coastal Trainers educate community leaders, business owners and elected officials about connections between coastal science, management and the local economy.  

Ongoing Research

Water Quality: Rookery Bay Reserve has five stations measuring various water quality parameters every 15 minutes, with monthly nutrient samples analyzed by the Florida DEP.

Sea Turtle Nesting Monitoring: Specialists and volunteers patrol beaches to protect sea turtle nests from predators during the nesting season.

Cultural Resource Management: Staff document and protect cultural resources using a new GIS-based database, facilitating targeted research and management planning.

Fisheries Monitoring: Monthly sampling efforts assess juvenile fish populations and habitat use, with a focus on fish and shark populations in the Ten Thousand Islands.

Shorebird Nesting Monitoring: Least terns and black skimmers nest in mixed colonies, with data collected weekly to protect these species and their habitats.

Marine Mammal Monitoring: Staff participate in the Marine Mammal Stranding Network, assisting with the rescue and rehabilitation of distressed marine mammals.

Sentinel Sites: The NERR System SSAM-1 monitors changes in sea level, inundation patterns and coastal vegetation using standardized protocols.

Mangrove Research and Monitoring: The Fruit Farm Creek Restoration Project monitors ecosystem changes to restore mangrove habitats affected by historic road construction.

Seed Banking with Naples Botanical Garden: A partnership with NBG aims to protect and conserve the Reserve’s flora by collecting and preserving seeds of underrepresented and at-risk plant species.

American Crocodile Nesting and Monitoring: In partnership with University of Florida Croc Docs, the small population of American Crocodiles is monitored annually to collect data and protect this threatened species.

Frequently Asked Questions

Year-round

Yes. Please visit the Rookery Bay Environmental Learning Center to learn about all the special events and educational programs, including a lunch & learn series, art reception nights, Festival of Birds, Rookery Bay Community Day, Wildlife and Watercolors Class, Birding with Biologists class, Photography Class, Forest Bathing and much more. The Friends of Rookery Bay offers guided-eco tours to get out on the water by boat and kayak. A variety of adventures are offered including Essence of the Estuary in the Back Bays, Barrier Island Shelling, Ancient Island Excursion, Sunset Bird Rookery Cruise and Sunset Beach Cruise. An ADA accessible boat is available as well.

Yes; must be on leash. In some areas, dogs are not allowed in Shorebird Nesting Sites in breeding season.

Follow current FWC saltwater fishing regulations: https://myfwc.com/fishing/saltwater/recreational/

Follow current FWC boating regulations: https://myfwc.com/boating/regulations/

Call Florida Fish and Wildlife Conservation Commission at 1-888-404-FWCC (3922).

Yes.

$10 for admission to the Rookery Bay Environmental Learning Center, $5 for children 3-12 and free for under age 3. There are other fees associated with Collier County managed access points for boaters. The Rookery Bay National Estuarine Research Reserve does not charge access fees for boaters or kayakers. Donations to the Reserve are accepted through the Friends of Rookery Bay.

To become a volunteer, please fill out a volunteer form and join a volunteer orientation.

Partner Groups

  • Friends of Rookery Bay: A citizen support organization that helps with fundraising, volunteer recruitment, coordinates kayak and boat ecotours and assists with management of the Rookery Bay Environmental Learning Center.
  • U.S. Fish and Wildlife Service: Co-manages a portion of CRTTIAP within the Ten Thousand Islands National Wildlife Refuge.
  • National Audubon Society: Leases wetlands and submerged lands to the Florida Department of Environmental Protection, which are managed as part of the reserve.
  • Florida Fish and Wildlife Conservation Commission: Manages wildlife and fisheries within the reserve, including designated Critical Wildlife Areas.
  • Collier County: Maintains public boat ramps that provide access to the reserve.
  • Florida International University: Partners with the reserve, contributing staff and expertise.
  • Naples Botanical Garden
  • University of Florida/IFAS
  • United Arts Council of Collier County
  • Paradise Coast Convention and Visitors Bureau
  • Collier County Public Schools
  • Conservancy of Southwest Florida
  • Florida Forest Service
  • Conservation Collier
  • Florida State Parks and National Parks
  • Naples Chamber of Commerce
  • Marco Island Chamber of Commerce
  • WGCU Media
  • Tourism Publications of Southwest FL
  • Florida Gulf Coast University