The Apalachicola National Estuarine Research Reserve (ANERR) conducts a variety of monitoring programs focusing on the Reserve System’s System-Wide Monitoring Program and water quality, Wetland and Water Level and marsh-related monitoring, habitat change, and biological sampling. The Reserve maintains a list of priority research issues and works with a large collaborative network to further knowledge of Apalachicola River and Bay system. The two main threats to the bay system are the upstream diversion of fresh water and increasing local coastal development and land use changes. In addition to the ANERR's own research and monitoring programs, the Reserve works to promote research within and adjacent to ANERR by outside investigators from universities, government agencies and private institutions. 

Water Quality Monitoring
ANERR installed the first continuously monitoring water quality dataloggers in the Reserve between 1992-1995. At present, seven stations are maintained in the lower Apalachicola River and Bay area. Every 15 minutes, they measure temperature, specific conductivity, salinity, dissolved oxygen, pH, water level and turbidity. Weather can strongly influence water quality and is also monitored from a station in the upper East Bay marshes with data collected every 15 minutes. Nutrient and chlorophyll a samples are collected monthly at each datalogger location plus nine additional sites. All data is publicly available from the National Estuarine Research Reserve System's Centralized Data Management Office and the nutrient and chlorophyll-a data is available from DEP's Watershed Information Network Database.

Trawling
ANERR's long-term trawling program is designed to look at juvenile fish and macroinvertebrate distribute in the bay and link changes in distribution to water quality and other physical parameters. Twelve sites were sampled from 2000-2012, and nine stations have been sampled 2014-present. The sampling program mimics the gear and procedures of a long-term study done in the bay from 1972 to 1984 by an FSU researcher as well as having many of the same sampling locations incorporated into the project. Stations represent a variety of habitat and salinity. Water quality and weather data is recorded at each site along with the biological data.

Wetlands and Water Level Program
The Apalachicola NERR is part of the National Estuarine Reserve System’s Wetlands and Water Levels Program (WWL), which tracks habitat response to changing water levels. Understanding changes in surface elevation is important for understanding the biological response of marsh, mangrove, and SAV habitats to long-term changes in local water levels and inundation patterns, sediment dynamics, as well as to discrete episodic inundation events. This program includes three components: 1) Surface Elevation Table (SET) stations at 22 locations throughout the lower river, bay, and barrier island areas, which measure change in the marsh surface elevation, 2) marsh vegetation monitoring at three locations, monitored yearly for species composition, cover, and more, and 3) porewater water quality associated with the vegetation locations. 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 America (along with Weeks Bay, Alabama, and Grand Bay, Mississippi).

Last Modified: Wednesday, Oct 14, 2026 - 01:22pm