http://sanctuaries.noaa.gov

Water Quality Monitoring Program

Water Quality Is Clearly Important to Marine Ecosystems

Most marine animals and plants go through their entire life cycle completely 

surrounded by seawater. Healthy marine ecosystems depend on good water 

quality to maintain their productivity and species diversity. Water quality has been a 

high priority for managers of the Florida Keys National Marine Sanctuary and the focus 

of extensive scientifi c research since Congress designated the sanctuary in 1990. As 

part of the sanctuary legislation, Congress directed the U.S. Environmental Protection 

Agency and the state of Florida to create the Water Quality Protection Program. In 1995, 

as part of the new program, scientists from Florida International University established 

the Water Quality Monitoring Program to track and analyze water quality in sanctuary 

waters.

Water quality is an overall evaluation based on a suite of measurements and analyses 

conducted in the fi eld and laboratory. Water temperature, salt content (salinity) and 

dissolved oxygen (DO) concentrations are some of the environmental factors 

measured by scientists. Signifi cant changes in these and other factors can have 

negative effects on marine life, including increased susceptibility to disease and even 

death. Marine organisms may become stressed when conditions change beyond what 

they are able to tolerate. 

Land-Based Nutrients Impact Marine Life

Scientists also routinely measure the nutrient content of the water, especially the 

different chemical forms of two plant nutrients: phosphorus and nitrogen. An excess of nutrients (also called nutrient 

enrichment, or eutrophication) promotes the growth of macroalgae or seaweed, which compete with coral for living space on 

the seafl oor. In the Keys, nutrients enter nearshore waters from land, through stormwater runoff and groundwater seepage. 

Groundwater carries sewage from underground septic systems to nearshore waters and canals through the porous limestone that 

forms the islands of the Keys. Nearshore tidal currents can then move nutrient-rich waters to where they affect coral reefs and 

seagrass meadows—marine communities that are adapted to low-nutrient waters and can be impacted by nutrient enrichment. 

Coral reefs and seagrass meadows thrive best in waters with very little turbidity, or cloudiness. Water turbidity is affected 

both by sediment stirred up from the bottom and by concentrations of phytoplankton—the collection of microscopic algae and 

photosynthetic bacteria living in the water. A phytoplankton population explosion, or bloom, can cloud the water, turning it green 

in color. Phytoplankton contain the green pigment chlorophyll-a, which allows them to produce their own food using sunlight and 

raw materials. Such blooms, which are fed by phosphorus, nitrogen, and other plant-growth nutrients, can increase water turbidity 

and block sunlight from reaching seagrass on the seafl oor. Turbid water is detrimental to most shallow-water corals because they 

need sunlight to aide their symbiotic algae (called zooxanthellae) in providing essential nutrition. Phytoplankton are not harmful to 

all marine life, though, as they are important part of the food web for many species.

Currents Connect All Waters in the Keys 

The entire South Florida region, including the Florida Keys, Florida Bay and the Southwest Florida Shelf, is connected by 

water currents. Tidal fl ows take place daily through the channels between the Keys and the bay and between the bay and the 

Gulf of Mexico. Two large surface currents, the Florida Current and the Gulf of Mexico Loop Current, along with the inshore 

currents of the shelf, also sweep across the region. Fresh water from the Everglades fl ows through Shark River Slough on 

Florida’s southwest coast and then southward toward Florida Bay. The Florida Keys and adjacent coral reef are at the center 

Coral reefs thrive in clear, low-nutrient waters.

Photo: FKNMS

Florida Keys National Marine Sanctuary

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

visit sanctuaries.noaa.gov

Principal Investigator: Dr. Joseph S. Boyer, Florida International University

Written by: Nancy Diersing, Florida Keys National Marine Sanctuary

Published: May 2009

of this complex and interdependent system of water movement. 

The quality of water affecting the reef is infl uenced by water 

fl ows in and around the Keys themselves, as well as by currents 

originating outside the region. 

Thirteen Years of Monitoring Yields Results 

The Water Quality Monitoring Program has been collecting 

water quality data from 154 stations since 1995. Program 

scientists have closely analyzed the period from 1995 to 2008 

for trends. Throughout these 13 years, nearshore waters in 

the Keys exhibited high levels of nitrate, an organic form of 

nitrogen found in plant fertilizers and sewage. In contrast, 

elevated nitrate concentrations were not present at sampling 

sites in the Tortugas. This distribution pattern suggests that 

an inshore source of nitrate is being diluted by ocean water. 

Although upgrades in sewage treatment have been occurring throughout the Keys in recent times, sewage is probably still entering 

nearshore waters through groundwater and may partially account for high nitrate levels near shore. 

Additionally, the area north of the Lower Keys exhibited high turbidity, chlorophyll-a and phosphorus levels, indicating that 

phytoplankton populations may be experiencing blooms. Waters fl owing from the Southwest Florida Shelf are thought to 

contribute to these conditions. Some of the highest nitrate levels are also observed at a few sampling sites in this same 

non-populated area. Instead of originating from sewage or fertilizers, these nitrates may be entering the water column when 

sediment containing nitrates and other organic material is stirred up from the shallow seafl oor on windy days. 

Geographic Trends Detected in Water Quality Characteristics 

Statistical analyses of the data identifi ed two major geographic trends. One trend was apparent from north to south: the 

highest chlorophyll-a, turbidity and dissolved nutrient levels were found north of the Middle Keys in sites nearest to the Southwest 

Florida Shelf. These levels gradually decreased moving south toward the Marquesas. This decline was probably due to the uptake of 

nutrients by marine life and by mixing with ocean waters. This north-south pattern is thought to be driven by waters from the shelf, 

which are high in phosphorus. 

The second major trend was evident from inshore waters near the Keys toward 

offshore waters on the ocean side. Nutrients gradually decreased from inshore 

stations along the Keys toward the offshore stations at the reef. This 

inshore-offshore pattern points to a land-based source of nutrients. Stations 

from the Tortugas, also with the lowest nutrient levels, were similar to reef 

stations along the Keys.

The highest phytoplankton populations in the region, as indicated by 

chlorophyll-a levels (left), were found outside of the sanctuary on the Southwest 

Florida Shelf. Chlorophyll-a levels diminished from the north to the south near the 

Marquesas and Tortugas. A similar trend was observed in total phosphorus, an 

important nutrient fueling the phytoplankton populations. Most likely, coastal 

rivers, runoff and Gulf of Mexico waters to the north contributed to the high levels 

of phosphorus observed in shelf waters. 

It’s All about the Big Picture 

By examining water quality monitoring results from sanctuary waters, along with results collected from nearby waters, scientists 

and managers have begun to understand the big picture of water quality. Through this regional approach, much has been learned 

about nutrient sources, the role of surface currents and geographic differences in water quality. In this interconnected system, 

water quality is affected by sources located within the Keys and as well as those outside of the Keys. Changes in fresh water 

fl ows on the mainland planned as part of the Comprehensive Everglades Restoration Program may also affect water quality in 

the future. By systematically monitoring the system, scientists will continue to provide sanctuary managers with the best available 

information. To view the many data maps and reports produced as part of the Water Quality Monitoring Program, 

visit http://serc.fi u.edu/wqmnetwork.

Shelf waters have the highest chlorophyll-a levels.

Image: FIU

The region is connected by surface currents. 

Image: FKNMS Science Report, 2001