Nassau-St. Marys Basin 

Lakes, Rivers, Streams, and Aquifers

Florida Department of 

Environmental Protection 

Division of Environmental Assessment 

and Restoration

Bureau of Assessment and Restoration Support, 

Watershed Monitoring Section

Good science is the foundation of the Florida Department of Environmental Protection’s (FDEP) 

programs to assess and protect water quality. FDEP is committed to characterizing the 

environmental conditions of Florida’s freshwater resources through several monitoring programs. 

The Watershed Monitoring Section administers the Status Monitoring Network, which oversees the 

statewide sampling of surface and ground water. This report summarizes the 2007 Status 

Monitoring Network results for the Nassau-St. Marys Basin. 

Nassau-St. Marys Basin

The Nassau-St. Marys Basin occupies approximately 1436 square miles in northeastern Florida, 

with part of the St. Marys Basin (643 square miles) located in southeastern Georgia. All or part of 

5 counties in Florida (Baker, Columbia, Duval, Nassau, and Union) and 3 counties in Georgia 

(Camden, Charlton, and Ware) are part of the Nassau-St. Marys Basin. The Nassau River forms 

the boundary between Nassau and Duval Counties just north of Jacksonville. The St. Marys River 

forms the border between southeast Georgia and northeast Florida. The St. Marys River, a 

blackwater stream that originates in the Okefenokee Swamp, extends 125 to 130 miles before 

discharging to Cumberland Sound and the Atlantic Ocean. 

The prominent land use and land covers in the Nassau-St. Marys Basin are silviculture, wetlands 

and forest, primarily managed pine forests. The population in the Nassau-St. Marys Basin is 

relatively low, with the highest population densities found in Fernandina Beach, Yulee, and 

Macclenny. Amelia Island is a popular tourist destination. Major industries in the area are farming 

(livestock and poultry), silviculture, and commodity production. The Nassau River and estuary 

support a healthy recreational and commercial fishing industry, especially commercial crabbing 

and shrimping.

Natural areas cover a substantial portion of the Nassau-St. Marys Basin. Some of the larger 

conservation and recreation lands include the Amelia Island State Park, Big Talbot Island State 

Park, Little Talbot Island State Park, Fort Clinch State Park and Aquatic Preserve, and Olustee 

Battlefield Historic State Park; Osceola Wildlife Management Area; Osceola National Forest and 

Cary State Forest; and Big Gum Swamp Wilderness. In addition to providing important habitat for 

wildlife, these natural areas provide ground water recharge, flood protection through the natural 

storage and detention of floodwaters, and the maintenance and enhancement of water quality. 

The following table summarizes land use statistics calculated for the Nassau-St. Marys Basin from 

2004 Statewide Land Use imagery.

Land Use Agriculture Forest Urban Wetlands Other

Percentage 4.2 49.9 5.9 33.1 6.9

The percentage reported as “Other” consists of water, rangeland, barren land, transportation, communication, and utilities.
Monitoring Design of the Status Monitoring Network

FDEP has worked with the water management districts, local governments, and other entities to 

establish an Integrated Water Resource Monitoring (IWRM) Program. This program combines 

surface and ground water monitoring efforts, consisting of water chemistry, biology, and sediment 

analyses. It is fiscally and logistically prohibitive to sample every river, stream, lake, or individual 

well in the state on a regular basis. A probabilistic monitoring design is a cost-effective approach 

to produce a statistically valid estimate of the condition of water resources. The IWRM Program is 

made up of three levels of monitoring designs: (1) the Status Monitoring Network designed to 

allow statistical inferences about all state waters; (2) more intensive basin monitoring used to 

identify and confirm impaired waterbodies that do not meet Florida’s water quality standards; and 

(3) site-specific regulatory compliance monitoring.

The Status Monitoring Network uses a random site monitoring design to assess the state’s surface 

and ground water quality. The objective of this design is to broadly characterize aquatic resources 

with a known statistical confidence. Samples are collected from randomly selected points, which is 

a cost-effective way to provide a geographic snapshot of the condition of all waters in a basin. This 

monitoring program is not designed to answer site-specific questions about individual lakes, rivers, 

streams, or wells.

The Status Monitoring Network categorizes Florida’s fresh waters into 6 different resource types. 

Four of these are surface water: small lakes, large lakes, rivers, and streams. The other 2 

resources are ground water: unconfined and confined aquifers. The 2004–09 Status Monitoring 

Network design divides the state into 29 basins, with 5 or 6 basins sampled each year. 

Approximately 30 samples are collected annually from each resource in the selected basins. Thus, 

in each basin, approximately 120 samples are collected for surface water resources, and 60 

samples for ground water resources, in addition to quality assurance samples.

Lakes

The Nassau-St. Marys Basin has approximately 10 lakes. FDEP has divided these lakes by size 

into 2 categories: small lakes of 2.5 to 25 acres and large lakes over 25 acres. This division 

allows a better characterization of the status of the basin’s lake resources. There are few natural 

small lakes found in the basin.

Rivers and Streams

The Nassau River, North Prong of the St. Mary’s River, and the St. Mary’s River, totaling 116

miles, represent the river resource. The remaining streams and tributaries are designated as the 

stream resource. These total about 605 miles, although some may be dry during periods of 

drought. Both resources can have different habitats and uses.

Aquifers Aquifers are permeable layers of sand, gravel, or rock that contain water. Unconfined aquifers are 

near the land surface and are easily affected by human activities. Confined aquifers lie below a 

layer of material, such as fine-grained clay, that limits the downward flow of water. Water in 

confined aquifers usually filters slowly through sediment and rock layers, and is older and less 

affected by human activities. FDEP’s Watershed Monitoring Section samples ground water in the 

Nassau-St. Marys Basin through wells in unconfined and confined aquifers. 

There are three major aquifer systems present throughout the entire Nassau-St. Marys Basin: the 

surficial aquifer system (SAS), the intermediate aquifer system (IAS), and the Floridan aquifer 

system (FAS). The SAS is the water table aquifer and is used as a potable water supply to a 

limited extent. The SAS is important in this watershed because it is the groundwater that directly 

interacts with surface waterbodies, providing base flow to streams, estuaries, and lakes. The IAS 

is composed of clays and acts mainly as a confining unit. The primary source of potable water in 

the basin is the FAS, which is deep, confined, and under artesian pressure throughout the area.
Summary and Results

The tables below show the sampling carried out for each resource in the Nassau St. Marys Basin, 

in terms of acres of large lakes, number of small lakes, miles of rivers and streams, and number of 

wells for confined and unconfined aquifers. Not all randomly selected stations can be sampled for 

various reasons. Those that can be sampled are termed accessible. Those stations that cannot 

be sampled are considered either dry or inaccessible. Reduced rainfall or periods of drought occur 

on a cyclical basis in many areas of Florida. Prolonged or intense periods of drought can 

adversely affect water chemistry. During the sampling period, precipitation was reduced by 11% 

compared with the 30-year annual average.

Surface Water Resource Large Lakes

(≥ 25 acres)

Small Lakes

(2.5–25 acres)

Rivers

(3 rivers/canals)

Streams

(all other streams/

canals)

Resource Size

(area, number, length) 2,874 acres 3 lakes 116 miles 605 miles

Accessible 100% 67% 46% 20% 

Dry 0% 0% 0% 8% 

Inaccessible 0% 33% 54% 72% 

Number of Samples 30 2 30 30

Ground Water Resource Unconfined Aquifers Confined Aquifers

Number of Wells 68 78

Accessible 50% 36% 

Inaccessible 50% 64% 

Samples 29 28

Basin Precipitation Average Annual

(1971–2000)

Annual

(2007) 

Nassau-St. Marys Basin 51.7 inches 46.0 inches

Rainfall data were obtained from the National Climatic Data Center database for the Fernandina Beach and Glen St Mary 1 W Stations. 

The discussion and figures below provide results for the basin’s surface and ground water 

resources for a number of important indicators (see the Definitions and Criteria pages for 

explanations of the indicators used). As discussed in Definitions and Criteria, natural conditions 

such as higher water temperatures, freshwater and stormwater inflows, and different soils can 

affect the results shown below. The exceedance of a standard or threshold is not necessarily 

caused by a pollutant.

Lakes: Dissolved oxygen (DO) is below the standard in 7% of the large lakes. Low DO can be 

harmful to aquatic life. Fecal coliform bacteria levels are within the standard for all large lakes. pH 

is within the standard range for the large lakes. Un-ionized ammonia levels are within the standard

for all large and small lakes. The Trophic State Index, a combined measure of nutrients and 

chlorophyll that indicates lake health, shows that 3% of the large lakes sampled have excess 

nutrients and chlorophyll. There were not enough data to assess small lakes. 

Rivers and Streams: DO is below the standard in 20% of the rivers and 87% of the streams 

sampled. Canal/ditch construction and ground water inflows can contribute to low DO 

concentrations. Low DO can be harmful to aquatic life. Fecal coliform bacteria are above the 

standard in 17% of the streams and within the standard for the rivers sampled. pH is outside the
For more information, contact:

Florida Department of Environmental Protection, Watershed Monitoring Section, MS 3525

2600 Blair Stone Road, Tallahassee, FL 32399

(850) 245–8433; http://www.dep.state.fl.us/water/monitoring/status.htm

standard range for 47% of the streams and within the standard for rivers. Low pH occurs naturally 

in blackwater streams, which are numerous in this basin. Un-ionized ammonia values are within 

the standards for rivers and streams. Chlorophyll values are above the standard in 3% of the 

rivers and 10% of the streams.

 

Aquifers: Exceedances of arsenic (3%), chromium (3%), and lead (10%) are found in a small 

percentage of the unconfined wells. An exceedance for sodium (4%) was found in the confined 

wells. Total coliform bacteria exceed the standard in 4% of the confined wells and are within the 

standard for unconfined wells. These bacteria are indicators of possible human health effects if the 

water is used for drinking. All other analytes are within standards.

Surface 

Water 

Resource

Dissolved Oxygen Fecal Coliform pH Un-ionized 

Ammonia

Trophic State 

Index

Large 

Lakes

Small 

Lakes ISD ISD ISD ISD ISD

Surface 

Water 

Resource

Dissolved Oxygen Fecal Coliform pH Un-ionized 

Ammonia Chlorophyll

Rivers

Streams

Ground 

Water 

Resource

Arsenic Cadmium Chromium Lead Nitrate–

Nitrite Sodium Fluoride Total Coliform

Unconfined 

Wells

Confined 

Wells

Note: The gray segments of the pie charts represent the percentage of water resources that meets water quality standards. Blue 

segments represent the percentage that does not meet the standards. See the Definitions and Criteria pages for more information.

ISD: Insufficient data for analysis.

This survey does not represent a comprehensive analysis of any individual waterbody. 

The Watershed Monitoring Section would like to thank the St. Johns River Water Management 

District for its contributions to this report.
Surface Water Definitions and Criteria 

Each indicator listed below was chosen because it has an applicable state criterion, found in Criteria for 

Surface Water Quality Classifications, Rules 62-302 and 62-303, Florida Administrative Code.

Indicators Criterion/Threshold1 Designated Use

Fecal Coliform Bacteria < 400 counts/100mL Recreation

Dissolved Oxygen ≥ 5 mg/L Aquatic Life

pH ≥ 6 and ≤ 8.5 SU Aquatic Life

Un-ionized Ammonia ≤ 0.02 mg/L Aquatic Life

Chlorophyll a ≤ 20 μg/L Aquatic Life

Trophic State Index (TSI) Color ≤ 40 PCUs, then TSI ≤ 40

Color > 40 PCUs, then TSI ≤ 60 Aquatic Life

1 mL – milliliters; mg/L – milligrams per liter; SU – standard units; μg/L – micrograms per liter; PCUs – platinum cobalt units

Fecal coliform bacteria: The single-sample threshold for fecal coliform is 400 counts per 100 milliliters of 

water. These bacteria can enter water through the discharge of waste from mammals and birds, agricultural 

and stormwater runoff, and untreated human sewage. The presence of fecal coliform bacteria may indicate 

that the water is contaminated by other disease-causing organisms.

Dissolved oxygen (DO): The state criterion for DO is a minimum of 5 milligrams per liter to maintain healthy 

conditions for aquatic life. Lower levels do not affect human recreation. Algae and plants produce oxygen 

through photosynthesis. Oxygen is also dissolved in water by wind and wave action. Respiration by aquatic 

animals, decomposition, wastewater, stormwater runoff from urban streets or farmland, and failing septic 

tanks consume oxygen. Natural conditions—such as ground water from springs, water from 

swamps/wetlands, higher water temperatures, and calm and cloudy weather—can also decrease DO levels 

in waterbodies.

pH: The surface water criterion for pH is between 6 and 8.5 standard units. The pH scale, which ranges 

from 0 to 14, is a measure of the degree of acidity or alkalinity of a solution. Numbers below 7.0 indicate 

acidity; numbers above 7.0 indicate alkalinity. The midpoint of 7.0 on the pH scale represents neutrality—

that is, a neutral solution is neither acidic nor alkaline. pH affects many chemical and biological processes in 

water, and aquatic organisms are adapted to a certain range of pH. When pH levels are outside this range, it 

stresses these organisms’ physiological systems and can reduce reproduction. Atmospheric deposition (acid 

rain), geology, vegetation, and pollution can cause changes in pH.

Un-ionized ammonia: The threshold for un-ionized ammonia is less than or equal to 0.02 milligrams per 

liter. This is calculated from total ammonia and adjusted for temperature, salinity, and pH. Ammonia occurs 

in different forms; water temperature and pH affect which form predominates at any given time in an aquatic 

system. Un-ionized ammonia can be toxic to fish and invertebrates.

Chlorophyll a*: The threshold for chlorophyll is less than or equal to 20 micrograms per liter. Chlorophyll is 

the pigment that allows algae and plants to convert sunlight into organic compounds during the process of 

photosynthesis. Excess nutrients, such as nitrogen and phosphorus, can stimulate algal blooms. Excess 

algae sink to the bottom and decay, using up the oxygen that other plants and organisms require to survive. 

High concentrations of chlorophyll reduce water clarity and limit the light available to shallow-water 

ecosystems.

Trophic State Index (TSI)*: TSI and chlorophyll are the primary measures used to assess nutrient 

impairment in a waterbody. There are two thresholds for TSI, based on the color of a lake. Dark-water lakes 

with a mean color greater than 40 platinum cobalt units (PCUs) are impaired when their annual mean TSI 

exceeds 60. Clear and low-color lakes with a mean color less than or equal to 40 PCUs are impaired when 

their annual mean TSI exceeds 40. TSI is measured using chlorophyll, nitrogen, and phosphorus 

concentrations. A 10-unit increase or decrease in the index represents a doubling or halving, respectively, of 

the number of algal cells present.

________________________________ 

* Both TSI and chlorophyll a are not standards, but thresholds used to estimate the impairment of state waters. These 

thresholds are used in the analysis of Status Network data, based on single samples in a basin at a predetermined time of 

year. The analysis and representation of these data are not intended to infer the verification of impairment, as defined in Rule 

62-303, Florida Administrative Code, in these waters.
Aquifer Definitions and Criteria

The table below shows the thresholds for eight indicators regulated under drinking water standards.

Indicators Criterion/Threshold1 Designated Use

Arsenic ≤ 10 μg/L Potable Water(drinking water)

Cadmium ≤ 5 μg/L Potable Water(drinking water)

Chromium ≤ 100 μg/L Potable Water(drinking water)

Lead ≤ 15 μg/L Potable Water(drinking water)

Nitrate–Nitrite ≤ 10 mg/L Potable Water(drinking water)

Sodium ≤ 160 mg/L Potable Water(drinking water)

Fluoride ≤ 4 mg/L Potable Water(drinking water)

Total Coliform Bacteria 

(counts per 100 milliliters)

≤ 4 (sample maximum) Potable Water(drinking water)

1 μg/L – micrograms per liter; mg/L – milligrams per liter

Arsenic, cadmium, chromium, and lead are all naturally occurring metals in the earth’s crust. These and 

other metals are used in manufacturing and can be produced and used in pesticides, preservatives, and 

industrial operations. They may enter water as a pollutant. Florida has primary standards (criteria) for these 

metals to protect human health. Excess levels in drinking water can cause adverse health effects. 

Nitrate–nitrite is used in fertilizer and is found in sewage and wastes from human and/or farm animals. 

Florida’s drinking water standard is 10 milligrams per liter (mg/L) for nitrate and 1 mg/L for nitrite. In addition, 

to allow for the fact that the toxicity of nitrate and nitrite is additive, the standard for the sum of nitrate and 

nitrite is 10 mg/L. In the long term, nitrates and nitrites have the potential to cause serious adverse effects in 

humans. 

Sodium (salt) has a drinking water standard to protect individuals who are susceptible to sodium-sensitive 

hypertension or diseases that cause difficulty in regulating body fluid volume. Sodium is monitored so that 

individuals on sodium-restricted diets may take the sodium in their water into account. Drinking water 

contributes only a small fraction (less than 10%) of an individual’s overall sodium intake. 

Fluoride, a natural element, is added to drinking water systems to reduce dental cavities. Prolonged 

exposure to levels above 4 milligrams per liter may result in crippling skeletal fluorosis, a serious bone 

disorder. Lower levels may cause dental fluorosis when children are developing teeth. In its moderate and 

severe forms, dental fluorosis is a brown staining and/or pitting of the permanent teeth. 

Total coliform bacteria are common in the environment and are generally not harmful. The presence of 

these bacteria in drinking water, however, is an indicator that disease-causing organisms may be present. 

The U.S. Environmental Protection Agency and Florida have set an enforceable drinking water standard for 

total coliform of 4 counts per 100 milliliters to reduce the risk of adverse health effects. Drinking water that 

meets this standard is usually not associated with a health risk from disease-causing bacteria and is 

considered safe.