http://sanctuaries.noaa.gov

15 Years of Water Quality Protection 

Florida Keys National Marine Sanctuary

Scientists sample water quality at 150 stations. 

Photo: Bernie Altmeier for FKNMS

Long-term Studies Focus on Seagrass, Corals and Water Quality 

For 15 years, the Water Quality Protection Program has been the guiding force for water 

quality improvements in the Florida Keys. Recognizing the importance of water quality 

for sustaining the coral reef ecosystem, the Florida Keys National Marine Sanctuary 

and Protection Act called for the implementation of the program with the establishment 

of the sanctuary in 1990. 

The purpose of the Water Quality Protection Program is to recommend actions that 

maintain and restore water quality needed to sustain healthy native plant and animal 

populations, using science as a basis for decision-making. As part of the program, 

scientists have been conducting three long-term monitoring studies in sanctuary 

waters: the Water Quality Monitoring Project*, Seagrass Monitoring Project* and the 

Coral Reef Evaluation and Monitoring Project**. In keeping with the principles of 

adaptive management, the program has undergone two independent scientific reviews 

over the years to improve coordination and meet managers’ information needs. 

Monitoring Tracks Changes and Supports Wastewater Upgrades

Monitoring programs track and describe changes within the Florida Keys marine 

ecosystem, providing information needed to better manage sanctuary natural resources. 

The Water Quality Monitoring Project, which has over 150 sampling sites, has detected 

elevated nitrates in nearshore waters since sampling began in 1995. Nitrate is a form of 

nitrogen commonly found in sewage and plant fertilizer. The presence of nitrate in the 

highly populated Keys and its absence in the unpopulated Dry Tortugas region suggests 

that land-based nutrients are still entering and persisting nearshore. While most of the 

Keys islands have undergone wastewater upgrades, the upgrades are not yet complete 

and nutrients from sewage still exist and can impact the system. 

Water quality project data have been essential in supporting wastewater upgrades to 

protect nearshore marine communities from nutrient enrichment. Information from the 

project supported the authorization by Congress of up to $100 million in federal funds 

to implement the Florida Keys Water Quality Improvement Program. Administered by 

the U.S. Army Corps of Engineers, the program has awarded nearly $42 million to local 

governments to implement county-wide advanced treatment systems in the Florida Keys. 

Water Quality Trends in Sanctuary Influenced at Regional Level 

The large scale of the Water Quality Monitoring Project has allowed scientists to assemble 

a broader view of the physical, chemical and biological factors affecting the South Florida 

marine landscape. It is now known that some of the water quality trends observed within the 

sanctuary are strongly influenced by hydrological and climatological conditions occurring 

outside sanctuary boundaries. Currents and tides can transport river waters from the 

Gulf of Mexico and Florida’s southwest shelf to the sanctuary. According to chlorophyll-a 

data collected throughout the region, the most intense and persistent phytoplankton 

(algae) blooms originate outside of the sanctuary on the shelf, where elevated phosphate 

levels fuel the blooms. 

*Based at Florida International University’s Southeast Environmental Research Center

**Based at Florida Fish and Wildlife Conservation Commission’s Florida Fish and Wildlife Research Institute

The Water Quality Protection 

Program is guided by an 

interagency water quality 

steering committee and is 

jointly administered by the 

U.S. Environmental 

Protection Agency and the 

Florida Department of 

Environmental Protection. 

Scientific support and 

expertise is provided by a 

technical advisory committee 

composed of water 

quality professionals and 

other scientists who are 

familiar with the natural 

resources in the sanctuary. 

A management committee 

composed of resource 

administrators advises the 

steering committee and acts 

as the liaison to the technical 

advisory committee.

http://floridakeys.noaa.gov/
To learn more about these and other accomplishments, 

visit sanctuaries.noaa.gov

Phytoplankton blooms also occur in nearby Florida Bay. When 

the tidal currents move through the channels between the Keys, 

algae-rich bay waters can reach the reef tract on the ocean 

side where they may block out sunlight needed by reef-building 

corals—animals adapted to warm, clear, low-nutrient waters. 

Seagrasses Detect Increasing Nutrients

The Seagrass Monitoring Project uses a variety of methods 

to track the condition of seagrass and other benthic plants 

in the sanctuary. One method involves analyzing seagrass 

leaves for their nutrient concentrations. Leaves are good 

indicators for nutrients in the water column because as the 

plant grows, it absorbs nutrients from the surrounding water. 

Nutrient enrichment can lead to the degradation or loss of 

seagrass habitat. Under such conditions, nutrient-loving plants 

like seaweeds are favored in place of seagrass. At this time, 

monitoring of seagrass coverage in the sanctuary has not detected any overall loss of seagrass habitat. However, in many places 

changes occurring in seagrass species are consistent with increased nutrient availability in the water column, indicating that the 

once-dominant turtle grass is gradually being replaced by plants that are tolerant of higher nutrient conditions. 

Coral Monitoring Tracks Corals, Octocorals, Algae and Sponges

Nearly 15 years of coral reef monitoring data have shown declines in live coral cover and species diversity within the sanctuary. 

Multiple stressors have contributed to these declines, including high sea surface temperatures, coral disease, bleaching and 

damage from hurricanes. The El Niño years in 1997 and 1998 resulted in high seawater temperatures, which caused widespread 

coral bleaching and subsequent mortality in reefs throughout the Caribbean, including the Keys. Cold fronts like those 

encountered during the winter of 2010 have also lead to widespread loss of corals. Even so, the cover of live octocorals (sea fans, 

sea whips), macroalgae, and stony corals all increased between 2008 and 2009, while sponge cover remained about the same. 

This was the first time that an annual increase in stony coral cover (from 6.5% to 7.3%) was recorded since coral monitoring began 

in 1995. 

Sanctuary is Protected from Harmful Vessel Sewage Discharge 

The information provided by the Water Quality Monitoring Project and Coral Reef Evaluation and Monitoring Project provided the 

scientific justification for designating state waters within Florida Keys National Marine Sanctuary a “no discharge” zone in 2002. 

This EPA designation prohibits the discharge of sewage (untreated or treated) from all vessels. In December 2010, the National 

Oceanic and Atmospheric Administration implemented a similar rule to cover all sanctuary waters, federal and state, and added 

that all marine sanitation devices on boats be locked to prevent discharge when boating in the sanctuary. 

Special Studies Contribute Toward Better Understanding of Ecosystem 

Over the years, a wide variety of short-term studies called “special studies” have been supported by the Water Quality Protection 

Program. These projects have contributed greatly to a better understanding of the ecosystem by providing critical information on 

topics like groundwater flows, wastewater discharges, water circulation and canal water quality. Special studies have also provided 

sanctuary managers with much needed information on coral disease, coral population dynamics, queen conch reproduction, and 

the effects of mosquito control pesticides on non-target species. 

Water Quality Protection Program is Basis for Management of the Marine Ecosystem

The extensive monitoring of coral reefs, seagrass meadows and water quality supported in Florida Keys National Marine Sanctuary 

allows managers to track the condition of sanctuary waters, including any changes that result from restoration of water flows in 

the Everglades and Florida Bay directly to the north. These scientific studies have also contributed to condition reports and other 

documents that help guide sanctuary management. The program has supported the conservation mission of the U.S. Coral Reef 

Task Force and program data are published regularly in task force reports. This program has been so successful in the Florida Keys 

that Monterey Bay National Marine Sanctuary has adopted its own Water Quality Protection Program. A comprehensive website 

supported by program funds makes all reports and long-term data sets available to resource managers, scientists and others. For 

more information, visit http://ocean.floridamarine.org/fknms_wqpp.

Principle Invesitagors: Joseph N. Boyer, Florida International University; James Fourquerean, 

Florida International University; Rob Ruzicka, Florida Fish and Wildlife Research Institute

Written by: Steven Blackburn, U.S. Environmental Protection Agency and Nancy Diersing, Florida Keys National Marine Sanctuary

Published: October 2011

Vessels are required to dispose of sewage at pumpout stations on land. 

Photo: FKNMS