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Like all Research Reserves, Rookery Bay Reserve conducts monitoring according to the National Estuarine Research Reserve System’s (NERRS) System Wide Monitoring Program. Research staff also monitors wildlife and habitats with local significance. Staff partners with local, state, and federal agencies, non-profit organizations, and academic institutions to augment monitoring efforts.

Much of the Reserve’s monitoring efforts were designed to determine the effects of freshwater entering the estuaries in the wrong amounts and at the wrong times. In the 1960's, a large residential neighborhood was created just north of the Ten Thousand Islands. A network of roads and 58 miles of canals were built, but the project was later abandoned. The failed development permanently altered the natural flow of freshwater to the estuaries of the Ten Thousand Islands: it arrives in the wrong amount and timing. The new canal system directed freshwater down one central canal and out to a bay. The result was three very different bays: one bay has too much freshwater, one bay too little, and one about right. To improve the distribution of freshwater throughout the Ten Thousand Islands bays (or estuaries), the Picayune Strand State Forest is being restored as part of the Comprehensive Everglades Restoration Plan. Upon completion, freshwater flow is expected to be more evenly distributed between the three bays, therefore allowing a diversity of plants and animals to survive in each bay.


Effects of Land Use Change on Fish and Invertebrate Populations

Monitoring Program

Research-Monitoring-Fish3Since 1996, Rookery Bay Research Reserve’s research team and volunteers have been analyzing the effects of land-use changes on fish and invertebrate populations. They collect fish samples with a trawl net each month in several bays, including Pumpkin, Faka Union, Fakahatchee, Naples, Moorings, and Rookery. The catch is transferred from the net into bins of water and then sorted so thatfish and commercially important shellfish, such as stone crabs, blue crabs and pink shrimp, are counted and measured before being returned to the estuary. The team also makes note of the quantity of macro algae and other organisms caught in the net. At each trawl site, water chemistry information is recorded, including salinity, dissolved oxygen and water temperature.

The trawls help inform the reserve's management as well as three projects:

  • Effect of Picayune Strand Restoration on Fish and Shellfish Populations in the Ten Thousand Islands
  • Monitoring the Fish Populations of Naples and Moorings Bays
  • Changes in Rookery Bay and Henderson Creek Fish Populations: A 40-Year Retrospective Study

Why this Matters

Research-Monitoring-FishBays or estuaries are like nurseries where young fish grow up before moving out into the Gulf of Mexico. Healthy estuaries, which have the right amount of fresh water flowing in at the right time, provide sea grass, oyster beds, red mangrove prop roots, and macroalgae that serve as hiding places and feeding grounds for young fish. Many of the same species that recreational anglers target in the Gulf, including snapper, grouper, and trout, start their lives here.

Without this monitoring program, the restoration team in charge of Everglades restoration would not be able to tell if or when their efforts resulted in more natural conditions downstream. The City of Naples and the community around Moorings Bay would not know whether their waters are providing good habitat for diverse fish communities. Also, the South Florida Water Management District would not know how canal system management changes are affecting marine life in Henderson Creek.

To learn more about some of the fish in Rookery Bay Reserve, check out our Wildlife and Wild Places page.

Sea Turtle Monitoring Archive

2018 Sea Turtle Nesting

Final Update Oct. 8, 2018

Nesting Locations   Nests Caged 
Total False Crawls Nests Complete
 This Year   Last Year  This Year Last Year This Year Last Year Disoriented
Keewaydin Island 356 433 433 518 345 53 1
Sea Oat Island  9 24 3 14 7 1 0
Kice & Cape Romano  175 135 167 127 147 70 0
10,000 Islands 96 125 139 116 82 66 0
Rookery Bay Totals 636 717 742 775 441 190  0 
Collier County Totals 1595 1635 1587 1988 1070 743 31

2017 Sea Turtle Nesting

FINAL update: 11/8/2017 - this year's hatching season was cut short by Hurricane Irma

Nesting Locations   Nests Caged
Total False Crawls Nests Complete
 This Year   Last Year  This Year Last Year This Year Last Year Disoriented
Keewaydin Island  430 426 518 692 53


Sea Oat Island  24 20 14 3 1 5 0
Kice & Cape Romano  135 207 127 259 70 94 0
10,000 Islands 125 171 116 274 66 102 0
Rookery Bay Totals 714 819 775 1070 190 451
Collier County Totals 1641 1968 1977 2517 742 1130 15

2016 Sea Turtle Nesting

Updated: 10/17/2016

Nesting Locations   Nests Caged
Total False Crawls Nests Complete
 This Year   Last Year  This Year Last Year This Year Last Year
Keewaydin Island  391 402 682 391 154* 157
Sea Oat & Coconut Island  20 26 3 16 5 0
Kice & Cape Romano  207 120 259 107 80* 37
10,000 Islands 171 82 272 112 68 45
Rookery Bay Totals 789 630 1216 626 307 239
Collier County Totals 1927 1510 2520 1435 787 707

* Nesting beaches on Keewaydin and Kice/Cape Romano experienced serious flooding as a result of Hurricane Hermine over Labor Day weekend. Seventy-two nests on Keewaydin and 58 nests on Kice & Cape Romano were observed as inundated or accreted. Monitoring will continue until season ends in October in the event any eggs from those nests survive.

2015 Sea Turtle Nesting

Read our interns' final report and senior thesis from the 2015 nesting season

Sea Turtles

turtle interns Rookery Bay Reserve resource management specialists work in cooperation with U.S. Fish & Wildlife Service Collier County Natural Resources and the Conservancy of SW Florida to preserve this threatened species. With much assistance from volunteers and summer interns, staff patrol the beaches of Sea Oat Island, Cape Romano, Kice Island, and other islands in the Ten Thousand Islands five days a week during nesting season to locate nests and place cages over them so that the eggs will be protected from predation by raccoons. Each nest contains between 80 to 120 eggs.

After roughly 60 days, baby turtles emerge from the nests under the cover of darkness and crawl to the water, swimming until they reach relative safety in seaweed beds before being swept away on currents across the sea. Resource managers follow up on each nest to document the number of hatched eggs to get a better understanding of nesting success.

Although cages cannot protect nests from inundation by high tides or fire ant predation, the incorporation of caging efforts has increased nesting success in the reserve tremendously. Rookery Bay Research Reserve staff rely on help from interns and volunteers to protect and monitor the nests inside reserve boundaries.

Catch up on our sea turtle interns' latest adventures at their blog

Additional support for this program is provided through the Friends of Rookery Bay's Adopt-a-Nest program. Learn more


Sea Turtle Nesting Update through June 17, 2019 

Nesting Locations   Nests Caged
Total False Crawls Nests Complete
 This Year   Last Year  This Year Last Year This Year Last Year Disoriented
Keewaydin Island 233 175 346 215 0 0 0
Sea Oat Island  11 5 7 0 0 0 0
Kice & Cape Romano  59 63 36 82 0 0 0
10,000 Islands 64 30 64 70 0 0 0
Rookery Bay Totals 367 273 453 367 0 0 0
Collier County Totals 925 682 984 728 0 0 0

Nest monitoring on Keewaydin Island is managed by the Conservancy of SW Florida. Nest monitoring in the Ten Thousand Islands is managed cooperatively with Ten Thousand Islands National Wildlife Refuge. Nesting totals courtesy of Collier County Parks and Recreation Department.

CLICK HERE to see a "real-time" dashboard of turtle nest discoveries and other turtle data on Cape Romano

Learn more about the sea turtles of the reserve.


Seagrass-1Research and Monitoring Efforts

Staff has been monitoring species abundance and diversity at several locations within the Reserve and has documented a decline. Monitoring efforts were conducted at Cape Romano during 1998-2005, 2010 and 2011, Hurricane Pass during 1998-1999, and Johnson Bay 2001-2009. These monitoring efforts were initiated to provide baseline data on the location and condition of seagrass beds within the Reserve. Fixed transects were monitored annually during the peak growing season, usually in July or August, using snorkeling gear. A modified Braun Blanquet monitoring technique was used. Data were collected every 5 meters along each transect using a 1 m2 quadrat composed of 100 10 cm2 cells. Data collection at each quadrat included species composition, species abundance, seagrass density, epiphyte density, blade length, sediment type and water depth. Ancillary data collection included water temperature, salinity, DO, depth, conductivity and secchi depth.


During 2002-2005, the Reserve collaborated with the University of South Florida to use side-scan sonar technology to map the benthic habitats and prop scars in Henderson Creek, Hall Bay, Rookery Bay, Pumpkin Bay, Faka Union Bay, Fakahatchee Bay and Cape Romano. The Reserve would like these areas mapped again for change analysis.

Seagrass-2In 2005, a study titled “A comparison of side-scan sonar and aerial photography for submerged aquatic vegetation mapping” was conducted on the Cape Romano shoals. The results indicated that both methods were effective in mapping SAV. However, the side scan sonar was able to detect prop scars whereas, the aerial imagery was not. The Cape Romano shoals are located in a dynamic coastal area so it was crucial that the aerial photography was collected during optimum conditions.

Graduate Research

During 2009-2011, a graduate student from Florida Gulf Coast University, Susan Denham, was awarded a NOAA Graduate Research Fellowship to conduct her thesis research “Light limiting factors affecting seagrass, Thalassia testudinum, at Cape Romano shoals within Rookery Bay National Estuarine Research Reserve”. Her data are still being analyzed but preliminary results suggest total suspended solids (TSS) and color dissolved organic matter (CDOM) were increasing light attenuation in the Cape Romano shoal area.

Shark Nurseries in the Ten Thousand Islands

shark researchShark Nursery Assessment Program

Since 1999, research staff have been conducting monthly assessments to gain an understanding of fish population size and estuarine habitat use in relation to hydrologic restoration in the Ten Thousand Islands watershed. A monofilament gill net and baited long lines are used to catch sharks and sawfish for a database of community composition and age ranges. Using a donated houseboat as home base, researchers monitor the nets and lines from two hours before until two hours after sunset. Sharks and sawfish are carefully brought into the boat to be identified, measured, sexed, weighed and tagged before release so that we can continue to learn about habitat use as the fish age. Water conditions, such as temperature, dissolved oxygen and salinity, are also recorded.

Acoustic Monitoring 

Acoustic monitoringAn acoustic monitoring program is now underway to complement this assessment. Five acoustic receivers have been deployed in one of the bays in the Ten Thousand Islands study area. The receivers will record the presence of any sharks, sawfish or other large fish with an acoustic tag that swim within a several-hundred-meter radius. The receivers will also record basic information from tags in use by partnering institutions who are conducting similar research, including FWC and Mote Marine Laboratory. The data will be downloaded from the receivers each month as part of the reserve’s ongoing fisheries assessment and will help fill gaps in our collective understanding of predatory fish movement and habitat needs along the coast.

Why This Matters

Sharks utilize shallow, protected estuarine bays to give birth to their young. These back bays provide young sharks with plenty of food and protection from potential predators, such as larger sharks. To gain an understanding of shark nurseries and relative distributions before, during and after the restoration of the Ten Thousand Islands watershed, reserve researchers began collecting shark demographic data on a monthly basis in May 2000. This may be the first study ever to address the effects of restoration on shark populations.

shark scientistsBull sharks (Carcharhinus leucas) are more tolerant of low salinities than other sharks, and freely move from marine to freshwater locations. Results to date indicate that bull sharks are by far the dominant species caught in the Faka Union Bay. Scientists hope to learn more about sharks by documenting the different types of sharks found in each location to determine how they react to changes in their environment.

Learn more about this project

Shark Research Partnerships

Over the years Rookery Bay Reserve has worked with various research partners to broaden the applications of this shark assessment program. One collaborative project, facilitated by the Shark Foundation, entails collection of genetic samples that assist researchers with the University of Miami and Stonybrook University to determine possible linkages with other shark populations around Florida and the Caribbean. Another collaborative project assisted the Florida Aquarium, Georgia Aquarium, and Shedd Aquarium in their analysis of stress levels in sharks following capture.

Learn more about this project

Shark Monitoring Also Tracks Sawfish

sawfish-tied-off-sIn 2002 and 2003, 11 juvenile sawfish were captured, tagged and released. Four of them were recaptures that were previously tagged. The growth data from all recaptures contributed to a publication/paper which showed a substantially faster growth rate than previous literature exhibited. Since 2012, 33 sawfish, including one possible adult female (15' in length), were captured, tagged and released. All sawfish except the one large female, were 8' long or less and assumed to be one or two years old. Southwest Florida estuaries are important nursery habitats for juvenile smalltooth sawfish. Sawfish are extremely dangerous and caution is paramount if you encounter any sized sawfish.

Learn more about sawfish

2016 Sawfish Graph

Shoreline monitoring

1998 2019 Keewaydin Shoreline 400Mapping the shoreline is one way Reserve staff uses GIS technology to monitor coastal processes and guide management activity. Each year, staff collect GPS locations along the vegetation line to map dynamic coastal areas such as Keewaydin Island.

Although Keewaydin Island has changed significantly over the years, our 2019 data shows little change. The island eroded 450 feet after Hurricane Irma and it hasn’t accreted back yet as shown by the 2019 shoreline. Historically, this map shows some considerable accretion, meaning that the island is growing longer from year to year. 

Learn more about Keewaydin Island.

System-Wide Monitoring Program

julie data 250Rookery Bay National Estuarine Research Reserve (NERR) is part of a national network of 28 reserves that represent a variety of biogeographically important estuarine ecosystems throughout the coastal United States. Collectively, these NERR sites provide unique opportunities to address research questions and coastal issues on a national scale. The reserves are united in their research efforts through the System-Wide Monitoring Program (SWMP).

SWMP was developed to nationally standardize long-term monitoring programs across all reserves. SWMP is comprised of three components: abiotic, biotic, and habitat monitoring. The abiotic monitoring efforts include water quality, nutrients, and meteorology. The biotic monitoring includes monitoring of submerged and emergent aquatic vegetation. The habitat monitoring involves mapping habitat types and detecting change over time using aerial imagery.

Data collection, data quality assurance and control and data archival are all standardized methods.

Real-time data site

Click to get real-time data

Graphing tools

Click to access data graphing tools



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