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Ecosystem Science Programs at Apalachicola National Estuarine Research Reserve Quick Links

Apalachicola National Estuarine Research Reserve (ANERR) has developed research priorities based on specific threats that currently confront ANERR and the Apalachicola River and Bay system. The two main threats to the bay system and their potential impacts are the upstream diversion of fresh water and increasing local coastal development and land use changes. Developing a research plan for the ANERR represents an especially daunting task due to the size of the Apalachicola River and Bay, as well as the diversity of species and habitats present. Therefore, it is especially important to promote research within and adjacent to ANERR by outside investigators from universities, government agencies and private institutions. Agencies, universities and institutions that have been heavily involved in research within or in cooperation with ANERR within the last five years include:

  • Florida State University (FSU)
  • Florida Agricultural & Mechanical University (Florida A & M or FAMU)
  • NOAA Coastal Services Center
  • U.S. Fish and Wildlife Service
  • Florida Fish and Wildlife Conservation Commission
  • Northwest Florida Water Management District
  • U.S. Geological Survey
  • NERRS Science Collaborative
  • Florida Forest Service
  • Franklin County Board of County Commissioners and its Planning Office

East Bay datalogger

Water Quality Monitoring

Staff have maintained four dataloggers in the bay on a continuous basis since 1995, measuring temperature, specific conductivity, salinity, dissolved oxygen, pH, water level and turbidity every 15 minutes. They are located at Dry Bar, East Bay and Cat Point approximately one foot off of the bottom with a second datalogger on the surface at the East Bay site. Weather conditions can have a strong influence on water quality and is also monitored from a station in the upper East Bay marshes. Nutrient and chlorophyll a samples are collected monthly at each datalogger location, plus nine additional sites.

Sorting through fish

Nicole and Jason sort through fish collected in the trawl.


The Reserve began a long-term trawling program in 2000 and now has more than a decade of monthly fish and benthic macro-invertebrate data at twelve sites. The sampling program mimics the gear and procedures of a long-term study done in the bay by an FSU researcher from 1972 to 1984 as well as having many of the same sampling locations incorporated into the project. Sixty trawls are performed monthly at these stations that have various habitat and salinity regimes associated with them (five at each site). Fish species, number and are determined from each site, along with water quality measurements.

Hatchling loggerhead sea turtles

Hatchling loggerhead sea turtles

Listed Species Monitoring - Sea Turtles

A long-term monitoring and management program for listed species has been in effect since the early 1990s. Sea turtle nests are monitored and protected on beaches within and adjacent to the Reserve by staff, volunteers, and other agencies, most of which is coordinated by the Reserve. Management of the nests includes predator control, fencing nests, working with the County on a lighting ordinance, monitoring lighting violations, and working with a local NGO on correcting lighting problems.

Nesting sandwich tern and eggs

Nesting sandwich tern

Listed Species Monitoring - Shorebirds

The Reserve monitors and manages colonial migratory bird species including least terns, black skimmers, Caspian terns, Royal terns, brown pelicans, gull-billed terns, and sandwich terns on various man-made causeways and islands (both natural and man-made) within the Reserve in association with the FFWCC, Franklin County and USACOE.

Salt marsh

Salt marsh

Sentinel Site

Apalachicola NERR has water level monitoring stations and is measuring the elevation of a marsh surface over time. Emergent vegetation transects are also being looked at to see the changes in species composition and density over an elevation change of a marsh. This is being done to see changes in the lower marsh plants as the sea level rises. Apalachicola is also part of the NOAA Sentinel Site Cooperative and a project monitoring the ecological effects of sea level rise in the northern Gulf of Mexico (along with Weeks Bay, AL and Grand Bay, MS).

Cape St. George Lighthouse

Taking a profile of Cape St. George Island in 2004 by the lighthouse (before it was moved)

Shoreline Monitoring

After Hurricane Opal hit in 1995, a shoreline erosion and dune recovery study was instituted to monitor changes in local shorelines, dune and vegetation loss and recovery, as well as impacts from natural events such as hurricanes. The research section monitors beach and bay shorelines on Cape St. George Island at six locations quarterly to determine shoreline changes.

Scientist measuring oysters

A researcher measures the growth of oysters.

Oyster Growth and Spatfall Monitoring

Oyster growth and spatfall have been monitored monthly since March 2004 at two of the most productive oyster bars in the bay, Cat Point and Dry Bar. Differences in growth and spatfall can be compared to different environmental conditions on either side of the bay.

Seagrass transect

Seagrass transect

Seagrass Monitoring

A seagrass monitoring program to determine seagrass distribution and abundance was started in 2002. Survey methods have changed over the years to develop a more precise monitoring program and ANERR is currently managing ten fixed sites within the bay twice a year, at the beginning and end of the growing season. At each location, seagrass species are identified and the percent coverage of each species is determined. Blade lengths are measured and epiphyte coverage is classified as clean, light, medium or heavy.

Apalachicola Research Reserve

Core Programs

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About Apalachicola NERR

Last updated: August 08, 2014

  3900 Commonwealth Boulevard M.S. 235 Tallahassee, Florida 32399 850-245-2094
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