Nutrient Criteria Technical Support Document Nassau-St Marys River Estuary

Draft 1 June 2010

Site Specific Information 

in Support of

Establishing Numeric Nutrient 

Criteria in the

Nassau-St. Marys Estuary

Division of Environmental Assessment and Restoration

Standards and Assessment Section

Florida Department of Environmental Protection

Tallahassee, FL 32399

August 27, 2010
Nutrient Criteria Technical Support Document Nassau-St Marys River Estuary

Draft 2 June 2010

Table of Contents

Table of Contents.............................................................................................................................................2

Executive Summary..........................................................................................................................................4

Geographical and Physical Description.............................................................................................................6

St. Marys River Watershed..........................................................................................................................7

Middle St. Marys River................................................................................................................................8

Lower St. Marys River..................................................................................................................................8

Nassau River Watershed .............................................................................................................................9

Sources of Nutrients ...................................................................................................................................... 10

Biological Summary ....................................................................................................................................... 10

Oyster Reefs.............................................................................................................................................. 10

Salt Marsh................................................................................................................................................. 11

Plankton.................................................................................................................................................... 12

Water Quality Data Sources and Studies........................................................................................................ 12

Waters on 303(d) List..................................................................................................................................... 13

Numeric Nutrient Criteria Recommendation.................................................................................................. 14

References..................................................................................................................................................... 19
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List of Tables

Table 1. Checklist of potential nutrient enrichment symptoms in Nassau-St Marys Estuary. 6

Table 2. Summary of physical/chemical and land use data for Nassau-St Marys Estuary and Basin. 9

Table 3. Summary of nutrient data analysis for Nassau-St Marys Estuary. 15

List of Figures

Figure 1. Nassau-St Marys Basin and Planning Units. 5

Figure 2. St.Marys Estuary, including surrounding urban areas, dischargers, and protected lands. 10

Figure 3. Annual geometric mean for total nitrogen, 1980-2004. 14

Figure 4. Annual geometric mean for total phosphorus, 1971-2004. 14

Figure 5. Annual geometric mean for chlorophyll-a, 1985-2004. 14

Figure 6. The log-linear plot of TN and TP load limits (g/m2/yr) vs. hydraulic loading (qs) adapted and 

improved from Steward and Lowe (2010) 15
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Draft 4 June 2010

Executive Summary

This report was prepared by the Florida Department of Environmental Protection (FDEP), in 

cooperation with local scientists, to support the development of site specific numeric nutrient 

criteria for the Nassau-St Marys Estuary. The primary purpose of the proposed numeric nutrient 

criteria is to protect healthy well-balanced natural populations of flora and fauna from the effects of 

excess nutrient enrichment.

The St. Marys Basin occupies approximately 1,585 square miles in southeastern Georgia and 

northeastern Florida, with about 942 square miles of the basin in Florida (St. Johns River Water 

Management District [SJRWMD], 1993). Figure 1 shows the boundaries of the Nassau–St. Marys 

Basin, including the individual planning units. The St. Marys Basin includes all or part of five counties 

in Florida (Baker, Columbia, Duval, Nassau, and Union) and three counties in Georgia (Camden, 

Charlton, and Ware). Roughly 86 percent of the entire basin lies within four counties (Baker and 

Nassau in Florida, and Camden and Charlton in Georgia), and 89 percent of the Florida portion is

found within these two counties (SJRWMD, 1993). The basin lies within the Coastal Plain 

physiographic region, which extends throughout the southeastern United States. 

The dominant land use and cover in the St. Marys Basin are silviculture and upland forest, primarily

managed pine forests (SJRWMD, 1993). Agriculture in the St. Marys Basin is a mixture of livestock 

and poultry operations and commodity production. The St. Marys River is a blackwater stream that 

originates in the Okefenokee Swamp and extends 125–130 miles before discharging to Cumberland 

Sound and the Atlantic Ocean. The St. Marys Inlet lies at the entrance to Cumberland Sound at the 

mouth of the river between Cumberland Island, Georgia, and Amelia Island, Florida. It is an 

important passageway for commercial, recreational, and naval vessels, providing access to St. Marys 

Harbor, Georgia, Fernandina Harbor (via the Amelia River), and the U.S. Navy Submarine Support 

Base at Kings Bay, Georgia.

The Nassau Basin occupies approximately 464 square miles. The Nassau River is a small river forming 

the boundary between Nassau and Duval Counties just north of Jacksonville. The basin comprises

predominantly forest and wetlands. Silviculture is the main land use in the basin. Small population 

centers occur at Yulee and Callahan, with more intense urban development in the Amelia Island 

area. The basin includes approximately 55 river miles and about 10 square miles of estuary, 

including the mouth of the Nassau River, South Amelia River, Sisters Creek, and Ft. George River. 

The Nassau River and estuary support a healthy recreational and commercial fisheries industry, 

especially commercial crabbing and shrimping. Two unimproved inlets lie between the St. Marys and 

the St. Johns Rivers: the Nassau River Inlet, between the southern tip of Amelia Island and the 

northern tip of Little Talbot Island, and the Ft. George Inlet, between the southern end of Little 

Talbot Island and Wards Bank (an extensive sandbank separating the Ft. George and St. Johns 

Rivers).Nutrient inputs include stormwater runoff, agriculture pollutants, silviculture, and

urban/suburban land uses; atmospheric deposition; sediment loading and turbidity from shoreline 

erosion, septic tanks and wastewater treatment facilities. 
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Oyster reefs and salt marshes are the primary aquatic resources in the Nassau-St Marys River 

Estuary, roughly analogous in form and function to seagrasses in other estuaries throughout Florida. 

Unfortunately, there is not a functional relationship between nutrient levels and oysters or salt 

marshes (as there is with seagrasses) that is appropriate for setting nutrient limits in the Nassau-St 

Marys. 

Figure 1: Nassau-St Marys Basin and Planning Units.
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Table 1. Checklist of nutrient enrichment symptoms in the Nassau-St Marys Estuary

Response Variable Observed 

historically?

Observed 

currently?

Explanation 

Low DO 

(hypoxia/anoxia)

No Yes Naturally low DO levels in many of the tidal creeks and 

rivers (NOAA 1996; Morton 2010; Meyers 2010).

Reduced clarity Yes Yes REVIEW ALBER ET AL. (2005) – may have information 

about this. Naturally occurring high turbidity and color

(blackwater river) contributes to reduced water clarity. 

Increased chlorophyll a 

concentrations

Yes Yes NOAA (1996) and DeVivo (2009) reported levels of 

chlorophyll-a: >5, <20 which is consistent with current 

values. Wetlands are thought to be major source of 

nutrients.

Phytoplankton bloom Yes No Skeletonema costatum blooms in 2001 in areas 

characterized by increased orthophosphate 

concentrations, the result of urban stormwater runoff in 

newly urbanized areas of both basins(Livingston 2010). 

Problematic epiphyte 

growth 

N/A N/A

Problematic macroalgal 

growth

No No Meyers 2010.

SAV community changes 

or loss

N/A N/A Deep water, high tidal velocities, naturally high 

turbidities, and highly colored water may have prevented 

SAV establishment as explained with regard to the 

Tolomato-Matanzas Estuary (Steward et al. 2010).

Emergent or shoreline 

vegetation community 

changes or loss 

No No Meyers 2010.

Oyster reef community 

changes or loss 

Yes No Extensive oyster reefs within the lower watershed

(Meyers 2010). 

Impacts to benthic 

community

Yes No Infaunal species richness and diversity indices were lower 

at stations in Amelia compared to cognate in Nassau 

indicating an adverse (probably toxic) impact of the mill 

discharges in this part of the Amelia system (Livingston 

2010).

Fish kills No No No significant differences were noted in fish indices in 

the Amelia over the 12-month study period (Livingston 

2010).

Zooplankton Yes No Reduced zooplankton numbers in the Amelia system 

were probably related to changes in phytoplankton 

rather than direct effects of ammonia since zooplankton 

species richness was not affected (Livingston 2010).

Geographical and Physical Description

The topography of the overall Nassau–St. Marys Basin is generally flat and low near the Atlantic coast and 

rises inland to the Duval Uplands, Trail Ridge, and Northern Highlands. The coastal lowlands are poorly 

drained and very sandy. Land and water elevations are usually higher in the west and decrease eastward 

toward the Atlantic Intracoastal Waterway. Drainage has developed a stream pattern characterized by 

many relatively short streams with headwaters in swampy areas. Runoff in the area is rapid despite the 

storage afforded by swamps, and most of the streams naturally go dry after fairly short periods of deficient 

rainfall. Ground water is the principal supply of fresh water, and some streams are sustained in dry

weather by wastewater effluent withdrawn originally from the Floridan aquifer through wells. The lower 
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reaches of many of the small streams are tidal, and reverse flow may occur several miles upstream from 

their mouths. This usually occurs during periods when the level of the ocean is rising and runoff is slight or 

nonexistent.

The basin is located in the temperate climate zone, but the climate tends to be more tropical than 

temperate. The year is divided into two seasons: the rainy season, from June through October, and the dry

season, from November through May. The average annual precipitation in the basin is approximately 53

inches, with the greatest rainfall occurring during the late summer months. The middle of the basin is 

dominated by poorly to very poorly drained soils. These areas comprise about 20 percent of the soil types 

in the basin. Approximately 20 percent of the basin is composed of marsh types. Somewhat poorly drained 

soils comprise about 45 to 50 percent of the soil types in the basin. Scattered about the basin are areas 

dominated by well-drained to moderately well-drained soils. These comprise 10 to 15 percent of the soil 

types in the basin (DPC, 1975). The population in the Nassau–St. Marys Basin is relatively low, although 

Amelia Island has developed as a popular coastal tourist destination. The highest population densities are 

found in Fernandina Beach and Macclenny. The cities of St. Marys and Kingsland (both in Camden County, 

Georgia, at the mouth of the river) are rapidly growing because of their association with Kings Bay Naval 

Base, the settlement of retirees, and ecotourism activity focused on the Cumberland Island National 

Seashore (St. Marys River Management Committee [SMRMC], 2003). 

The Nassau–St. Marys Basin contains numerous surface water bodies. Surface waters, including lakes, 

streams, wetlands, and springs, occupy approximately 44.3 square miles, or about 3 percent of the total

basin area. This section delineates the basin’s hydrology, describes the movement and management of 

water in the basin, briefly describes the major characteristics of surface waters that influence water quality 

in the basin, and describes surface water classifications and special designations.

Two unimproved inlets lie between the St. Marys and the St. Johns Rivers: the Nassau River Inlet, between 

the southern tip of Amelia Island and the northern tip of Little Talbot Island, and the Ft. George Inlet, 

between the southern end of Little Talbot Island and Wards Bank.

St. Marys River Watershed

The upstream boundary of the St. Marys Basin is the Okefenokee Swamp. The main stem of the St. Marys 

River, a blackwater stream, is the principal surface water resource, with an annual average flow of about 

1,400 cubic feet per second (cfs) at its mouth (Georgia Department of Natural Resources [GDNR], 2002). It 

forms the border between southeast Georgia and northeast Florida. Hydrologically, the St. Marys Basin is 

divided into three subareas based on hydrologic functions: (1) a headwaters subarea with large floodplain 

wetlands that provide substantial storage; (2) a middle St. Marys subarea characterized by narrow 

floodplains confined to the main stem of the river; and (3) a lower St. Marys subarea that is tidally 

influenced and poorly drained (SJRWMD, 1993). 

The St. Marys River is a remote blackwater stream with an extensive marsh system. Beginning in the peat 

bogs of the Okefenokee Swamp, it empties into Cumberland Sound and the Atlantic Ocean. The lower

portion of the river is tidally influenced, and reverse fl ows occur daily (SJRWMD, 2000). Other major 

waterbodies in the basin include Amelia River, Cedar Creek, Deep Creek, Egans Creek, Little St. Marys 

River, Turkey Creek, and Ocean Pond.
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The major environmental stressors include oxygen-demanding substances, bacterial contamination, 

stream channel modifications and alterations of physical habitat (Georgia Department of Natural 

Resources [GDNR], 2002). Significant potential sources of environmental stressors in the basin include 

point source discharges, such as municipal and industrial wastewater and storm sewers, and nonpoint 

sources resulting from diffuse runoff from urban and rural land uses.

The predominant land use in the basin is silviculture. Amelia Island has developed as a popular coastal 

tourist destination. Local municipalities in Florida include Baldwin, Glen St. Mary, Macclenny, Fernandina 

Beach, and Hilliard. Those in Georgia include Folkston, St. Marys, and Kingsland.

In the Georgia portion of the basin, a 1988–90 land cover interpretation showed approximately 82 percent 

of the basin as forest cover and wetlands (GDNR, 2002). Within the SJRWMD portion of the basin, 85.8 

percent of the basin consists of forests and wetlands (SJRWMD, 2000). In the District Water Management 

Plan (SJRWMD, 2000), the district identifies the following future land use considerations: continued urban 

development is expected in the Amelia Island and Macclenny/Glen St. Mary areas; and large areas, 

particularly along the Middle Prong of the St. Marys River, are slated for suburban development.

The headwaters subarea includes the southern and western parts of the St. Marys Basin and extends to 

the point where the river turns northward, northeast of Macclenny. The eastern boundary runs along the 

top of the Trail Ridge. The subarea includes portions of the Okefenokee Swamp and the Osceola National 

Forest. The largest municipality is Macclenny. The subarea includes the following tributaries of the St. 

Marys River: North Prong, Middle Prong, Cedar Creek, South Prong, Deep Creek, and Baldwin Bay–Brandy 

Branch. The subarea is characterized by large floodplains in tributary headwaters and serves an important 

storage function for wetlands.

Middle St. Marys River

The major tributary in the subarea is Spanish Creek in Georgia. Most of the tributaries in the Middle St. 

Marys are short and originate on the Trail Ridge. The Suwannee Canal is located in this subarea, flowing 

from the Okefenokee Swamp east through the Trail Ridge and joining the river in the north portion of the 

subarea. This portion of the river runs northward and is characterized by floodplains confined to river 

margins and bluff erosion near small tributaries. The only lake of significance (100 acres or larger) in the 

basin is Hampton Walker Lake, which lies in this subarea.

Lower St. Marys River

The major tributary in the subarea is the Little St. Marys River. Floodplains cover approximately 50 percent 

of the land area. Tidally influenced flows have been measured as far as 21 miles upstream (SJRWMD, 

1993), although others have measured tidal influences as far as 64 miles upstream (George Varn, Jr.,

personal communication). The low topography and slope of the subarea, combined with tidal effects, 

make this the most poorly drained of the three subareas. Poor drainage has limited development in much 

of the lower St. Marys River, primarily due to the lack of soil suitability for septic systems in the floodplain 

areas. Higher banks in this area are moderately suitable for septic systems and these areas have been 

developed.

The data analyzed and presented in this report is for the Lower St. Marys River.
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Nassau River Watershed

The main drainage feature of the Nassau Basin is the Nassau River, with its numerous tributaries. The 

Nassau River is a small river forming the boundary between Nassau and Duval Counties. Other major 

waterbodies include Alligator Creek, Ft. George River, Lofton Creek, Mills Creek, Plummer Creek, Pumpkin 

Hill Creek, Sisters Creek, South Amelia River, and Thomas Creek.

Hydrologically, the Nassau River Basin can be divided into a riverine and an estuarine portion. A major 

subarea within the Nassau River watershed, the estuarine area, is known as the “Sea Islands,” an area that

runs along the coast from the St. Johns River north to the Santee River in South Carolina. The name is 

derived from the chain of barrier islands, which is separated from the mainland by meandering tidal creeks 

resulting from fluvial and tidal sedimentation in derelict lagoons or coastal-parallel marshes between 

beach ridges. The area consists of a vast saltmarsh estuary with numerous interconnecting tidal creeks and 

channels as well as minor uplands (“tree islands”). Very little has been documented about the upper,

riverine, portion of the basin. The extent to which tidal influence is felt upstream varies with rainfall, tides, 

winds, and evapotranspiration. There are no lake areas identified in this basin. The following is a list of 

Outstanding Florida Waters in the Nassau-St Marys Basin:

• Ft. Caroline National Monument Okefenokee National Wildlife Refuge

• Big Talbot Island State Park Amelia Island State Recreational Area

• Little Talbot Island State Park Fort Clinch State Park and Aquatic Preserve

• Nassau Valley State Reserve Waters within the Osceola National Forest, including Deep Creek, 

Middle Prong St. Marys River, and Ocean Pond

• Ft. George Island

• Nassau River–St. Johns River Marshes Aquatic Preserve

• Timucuan Ecological and Historic Preserve

The only identified spring in the basin is Su-No-Wa Spring in Nassau County. The enclosed spring, which

has an average discharge of 0.0145 cfs, is located near the head of Thomas Creek in the upper end of the 

coastal drainage area between the St. Marys and St. Johns Rivers (Osburn et al., 2002). Ground water is the 

primary source of drinking water in the St. Marys Basin; it is primarily supplied from the Floridan aquifer 

system (GDNR, 2002).

Table 2. Summary of physical/chemical and land use data for Nassau-St Marys River Basin.

Physical Characteristic Values Source

Mean depth 6.1 m Dame et al. 2000 and 

NOAA navigation 

charts

Tidal range 2-3 m Livingston 2010

Mean freshwater residence time 2-29 days Scavia and Liu (2009)

Watershed Land Use (2004)

Water/Wetland 21.31% SJRWMD 2000

Range/Forest 39.1% SJRWMD 2000

Urban 2.47 SJRWMD 2000

Agriculture 2.61 SJRWMD 2000

Unknown (no data) 25.7 SJRWMD 2000
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Sources of Nutrients

Potential nonpoint sources of pollution in the basin include stormwater runoff, agriculture pollutants 

leeching into groundwater, silviculture, and urban/suburban land uses; atmospheric deposition; sediment 

loading and turbidity from shoreline erosion; and septic tanks. Septic tanks are prevalent in some areas of 

the basin and have been identified as a potential source of nutrients (nitrogen and phosphorus), 

pathogens, and other pollutants that can pose a threat to public health (SJRWMD 2003). Surface waters 

can be adversely affected directly by system drainfields washed away by floodwaters or via runoff from 

areas where system failures result in ponding of untreated or inadequately treated wastewater on the 

ground. Surface waters can be adversely affected indirectly through seepage of groundwater 

contaminated by system discharges.

In Georgia, there is currently one permitted major municipal wastewater discharge with a flow greater 

than one million gallons per day (mgd). There are also six minor discharges (flow less than one mgd). 

Additionally, there are relatively few industrial wastewater discharges, including one major facility (GDNR, 

2002).

Within Florida, there are a number of domestic and industrial wastewater facilities in the St. Marys Basin 

with National Pollutant Discharge Elimination System (NPDES) permits to discharge to surface waters. 

There are seven active and one closed (Northeast Florida State Hospital Wastewater Treatment Plant 

[WWTP]) NPDES-permitted facilities in the Upper St. Marys River planning unit. The most significant of the 

active facilities is the Macclenny Waste Water Treatment Facility (WWTF). There are five active NPDESpermitted facilities in the Lower St. Marys River planning unit. The most significant of these are the 

Rayonier, Inc. and -Jefferson Smurfit Corporation pulp mills, and the Fernandina Beach WWTF (Figure 2). In 

addition, there are eight non-NPDES-permitted domestic and industrial waste facilities in that basin. There 

are no permitted domestic or industrial waste facilities with discharges to surface water in the Middle St. 

Marys River planning unit. There is one delisted Superfund site (Yellow Water Road) in the Upper St. Marys 

River planning unit. It is located in Baldwin within Duval County.

There are two active landfills in the Georgia portion of the St. Marys Basin but no active landfills in the 

Florida portion of the basin. There are seven closed landfills (one Class I, five Class II, and one 

Construction/ Demolition site) in the Upper St. Marys River planning unit, and one closed landfill (Class II) 

and one inactive landfill (Class III) in the MiddleSt. Marys River planning unit.

Biological Summary

The biological communities that characterize the vast majority of the aquatic habitat in the Nassau-St 

Marys River Estuary are tidal marshes and oyster reefs (Steward 2010). Water quality data suggest that

maintaining current nutrient loads will achieve a chlorophyll-based light transparency target that is the 

optimal method for numeric nutrient criteria development. 

Oyster Reefs

Oyster reefs are a major aquatic community in the Nassau-St Marys River Estuary and serve to locally 

decrease turbidity by trapping sediment. They present a dynamic community forming refugia, nursery 

grounds, and feeding areas for a variety of other estuarine organisms. Oysters provide hard substrate and 

habitat for many other species including, mud crabs (Rhithropanopeus harrisii), blue crabs (Callinectes 

sapidus), and amphipods. 
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Figure 2: St. Marys Estuary, including surrounding urban areas, dischargers, and protected lands.

A three year study was conducted in the nearby GTM Estuary looking at oyster growth rates at two sites 

with different nutrient loading scenarios and found that density, length, and biomass increased in oyster 

communities with higher nutrient loads suggesting that the oyster communities were capable of 

assimilating current nutrient loads while responding positively to increases in nutrient loads at least to 

current levels (Dix unpublished presentation, 2010). 

Salt Marsh

Salt marshes are another common community type in the HRE. Dominant plants include saltmarsh 

cordgrass (Spartina alterniflora), black needlerush (Juncus roemerianus), Glasswort (Salicornia spp.), and 
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saltwort (Batis maritima). This habitat supports a large population of infaunal organisms as well as a 

variety of transient fish and wildlife. 

McFarlin (2008) looked at the impact of fertilization on food webs in 19 coastal estuaries in Georgia and 

found that fertilization increased cover, height, and biomass of Spartina and the height of Juncus, but 

decreased Juncus cover and biomass. The study also showed increases in herbivores (grasshoppers) with 

fertilization, but little to no effect on decomposers (fungi) or detritivores (snails). In comparisons between 

fertilized plots and control plots, variation among sites was typically greater than the effects of 

fertilization. These results suggest that increases in nutrients at any particular site might be hard to 

distinguish from natural variation among sites and that increased nutrients are likely to have a stimulatory 

effect on plants and herbivores.

Plankton

Livingston (2002) conducted an evaluation of the effects of ammonia discharged by a pulp mill on 

estuarine plankton and other biological communities in the Amelia River-estuary in 1994-1995 and after 

restoration in 2000-2001. Data indicated that ammonia concentrations were significantly higher than 

those taken in the reference system (Nassau Estuary). Significantly reduced chlorophyll a concentrations 

were noted. There were periodic reductions of light transmission in areas affected by mill effluents and in 

upper areas of both estuaries. Field surveys indicated that whole water and net phytoplankton numbers 

and species richness were significantly lower in the Amelia system. Zooplankton numbers were 

significantly lower at various Amelia stations, whereas there were no significant differences in zooplankton 

species richness between the two study areas. The field results indicated that the most likely system-wide 

differences of water quality that could account for the noted biological responses were the relatively high 

ammonia concentrations in the Amelia system. Field ammonia levels in the Amelia system were 

significantly associated with observed impairment of key indices of phytoplankton assemblages in areas 

affected by mill discharges, especially during summer periods of maximal impact. The pulp mill undertook 

a restoration program based on the results of this work and in a follow-up investigation in 2000-2001, no 

significant associations of phytoplankton or zooplankton community health effects and ammonia were 

noted. However, there did appear to be reductions in phytoplankton and zooplankton with elevated 

orthophosphate, total phosphorus, silica, color, Secchi depths and temperature thought to be the result of 

stormwater runoff from upland sources (Livingston 2010).

Water Quality Data Sources and Studies

The assessment of water quality in the Nassau–St. Marys Basin includes an analysis of quantitative data 

from various sources, these include the:

• U.S. Environmental Protection Agency’s (EPA) Legacy and “new” STORET 

• U.S. Geological Survey (USGS)

• Florida Department of Health (DOH)

• Florida Department Environmental Protection (FDEP), 

• St. Johns River Water Management District (SJRWMD), 

• City of Jacksonville/Duval County, 

• National Park Service (NPS),

• Georgia Environmental Protection Division (GEPD) (mainstem of St. Marys River only)
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Waters on 303(d) List 

According to the Georgia 2000 305(b)/303(d) list, five out of nine waters within the St. Marys River basin in 

Georgia partially supported their designated uses, while four out of nine did not support their designated 

uses (GDNR, 2002). The Georgia list does not differentiate waters in the basin into separate planning units. 

Nonpoint sources are the primary source of pollution affecting waters in the St. Marys Basin. TMDLs were 

established for nine 303(d) listed waters in the Georgia portion of the basin in 2001, primarily for fish 

consumption and DO (GDNR, 2002).

The most common parameters listed for impairment in the Nassau–St. Marys Basin include mercury 

concentrations in fish and bacteria. These waters are on the Verified List of impaired waters (Table 4).

The headwaters and headwater streams that flow into the St. Marys River are naturally characterized by 

high acidity and color, and occasionally by low DO. This is especially noticeable during the summer months 

due to accelerated decomposition in adjacent swamps, particularly the Okefenokee (St. Marys River 

Management Committee [SMRMC], 2003).

As required by the IWR, the Department must identify the pollutants causing or contributing to dissolved 

oxygen (DO) exceedances in order to place DO on the Verified List. If a water segment is on the Verified 

List for both DO and nutrients, nutrients are identified as a pollutant contributing to DO exceedances. 

Occasionally, low DO concentrations observed in surface waters are the result of natural conditions, and 

cannot or should not be associated with a pollutant. This is typically found in systems that exhibit black 

water characteristics. The Department believes that the low DO observed in several of the St. Marys River 

segments and its major tributaries are due to natural conditions and are not being caused by a pollutant. 

These waterbodies exhibit blackwater characteristics (dark color, low DO, high organic content, low 

conductivity, etc.). In most of these segments, the BOD and nutrient levels were at or below acceptable

threshold levels. 

Table 4. 303(d) list of impaired waters within the marine portions of the Nassau-St Marys basin.

Basin Group 

Name

Planning 

Unit

Waterbody 

ID (WBID)

Water Segment 

Name

Parameters 

Assessed (IWR)

Concentration Causing 

Impairment

Nassau - St. 

Marys

Lower St. 

Marys River 

2106 Little St Marys River Mercury (In Fish 

Tissue)

Exceeds DOH Threshold 

(>0.43 Mg/Kg)

Nassau - St. 

Marys

Lower St. 

Marys River 

2140 Jackson Creek Shellfish 

(Coliforms)

Exceeds SEAS 

Thresholds

Nassau - St. 

Marys

Nassau River 2149 South Amelia River Shellfish 

(Coliforms)

Exceeds SEAS 

Thresholds

Nassau - St. 

Marys

Nassau River 2153 Alligator Creek Total Coliforms >2,400 Colonies / 100 

Ml

Nassau - St. 

Marys

Nassau River 2156 Unnamed Branch Dissolved 

Oxygen

< 5.0 Mg/L

Nassau - St. 

Marys

Nassau River 2156 Unnamed Branch Fecal Coliforms >400 Colonies /100 Ml

Nassau - St. 

Marys

Nassau River 2156 Unnamed Branch Total Coliforms >2,400 Colonies / 100 

Ml

Nassau - St. 

Marys

Nassau River 2157 Little Mill Creek Total Coliforms >2,400 Colonies / 100 

Ml

Nassau - St. 

Marys

Nassau River 2174 Nassau Sound Shellfish 

(Coliforms)

Exceeds SEAS 

Thresholds
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Numeric Nutrient Criteria Recommendation

Data was received from the IWR database from 1971 through 2004 (Not every station had sufficient data 

for each year, so stations were pooled). For all combined stations, annual geometric means were 

calculated for TP, TN, and chlorophyll a (Figures 3-5). The distributions of the geometric means are shown 

in Table 3. For all sites, the long term mean annual geometric mean was calculated, and a lognormal 

distribution function was fit, to estimate the long-term 75th and 90th percentile of the data. 

Figure 3. Annual geometric mean for total nitrogen, 1980-2004.

Figure 4. Annual geometric mean for total phosphorus, 1971-2004.
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Figure 5. Annual geometric mean for chlorophyll-a, 1985-2004.

Table 3. Summary of data analysis for Nassau-St Marys Estuary, all stations combined (period and 

number of record varied among analytes). LN = natural logarithm, GM = geometric mean, C.I. = 

confidence interval. Long term geometric means and the 90th

Statistics

percentile of annual geometric means are 

highlighted. 

Chlorophyll-a TN TP

Log Normal 

Distribution

Empirical 

Percentile

Log Normal 

Distribution

Empirical 

Percentile

Log Normal 

Distribution

Empirical 

Percentile

Mean LN TP 0.76 6.46 4.37

Std. Dev. LN TP 0.54 0.37 0.33

N (Years) 5 11 20

95% C.I. 0.68 0.25 0.15

Long-term GM 2.15 2.40 636.99 673.24 79.36 83.48

Lower 95% C.I. 1.09 497.39 68.16

Upper 95% C.I. 4.23 815.78 92.40

75th Percentile 3.10 2.51 816.58 830.36 98.81 94.73

90th Percentile 4.32 3.60 1021.14 885.81 120.37 120.97

A general nutrient model was applied to the St. Marys to predict limits or acceptable ranges of nutrient 

loadings and concentrations related to a desirable trophic state (mesotrophy or oligotrophy). It is an 

empirically defined relationship between water residence times and nutrient loading limits for 

mesotrophic Florida systems (Steward and Lowe 2010). Initial results (Figure 6) show that the line of best 

fit lies along the upper mesotrophic boundary. If, based on healthy biological communities, the 

waterbodies are meeting their designated uses, the trophic positions of the points in the graphs could be 

used as a basis for nutrient criteria, and the current TN and TP loadings can be considered the loading 

limits.
Nutrient Criteria Technical Support Document Nassau-St Marys River Estuary

Draft 16 June 2010

Figure 6. The log-linear plot of TN and TP load limits (g/m2

/yr) vs. hydraulic loading (qs) adapted and 

improved from Steward and Lowe (2010) by the incorporation of additional data points from 

mesotrophic estuaries initially used to validate the models. A point lying above the 95% confidence 

interval for the line-of-best-fit (=upper mestrophic line or UML) is considered eutrophic; below the lower 

mesotrophic line (LML) is considered oligotrophic. 

Proposed Numeric Nutrient Targets 

Methodology 

For consistent application and for providing an appropriate level of protection, water quality criteria need 

to include magnitude, frequency, and duration components. The magnitude is a measure of how much of 

a pollutant may be present in the water without an unacceptable adverse effect. Duration is a measure of 

how long the pollutant may be above the magnitude, and frequency relates to how often the magnitude 

may be exceeded without adverse effects. It is preferred to derive the magnitude component of a

criterion through a cause-effect relationship (such as those measured through toxicity testing). The 

magnitude would then be set at a level that would protect a majority of the sensitive aquatic organisms 

inhabiting the system. Absent a demonstrated cause-effect relationship, the magnitude may be set at a 

level designed to maintain the current data distribution, accounting for natural temporal variability, when 

the current conditions are protective of the designated uses of the waterbody. Since a criterion derived 

based on the existing data distribution has no direct link to any observed cause and effect relationship, it is 

assumed that maintaining the current data distribution will preserve the uses associated with that 

distribution.

The frequency and duration components of the criteria are best established as additional descriptors of 

the reference condition data distribution. Specifically, these components should be part of a statistical 

test designed to determine whether the long-term distribution of data has shifted upward ( or in some 

cases, downward) from the reference distribution. This test would then be used to determine whether 

future monitoring data are consistent with the magnitude (long-term average) defined by the reference 
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dataset. It is critical to account for the natural variability surrounding the magnitude expression and to 

control for statistical errors.

The derivation of the magnitude, frequency and duration components of the numeric nutrient criteria for 

TME is described briefly below. More details concerning the statistical approaches used can be found in 

the document “Overview of FDEP Approaches for Nutrient Criteria Development in Marine Waters” (FDEP 

2010).

Magnitude 

The magnitude component can be set at a variety of values based on the frequency and duration that will 

be used to determine compliance. For the “healthy existing conditions” approach, FDEP established the 

magnitude at: a) an adjusted long-term central tendency (geometric mean) of the distribution, expressed

as a long-term geometric mean never to be exceeded; and b) an annual geometric mean, not to be 

exceeded more than two times over a five- year period. The long-term average condition was adjusted to 

a level that represents an insignificant increase from the baseline. Allowing for an insignificant increase 

accounts for uncertainty in the estimate of the mean and partially addresses the fact that the reference 

based approach fails to identify a threshold of imbalance, and thus is highly prone to excessive Type I 

error. For the purpose of antidegradation evaluations, EPA has established that a ten percent change in a 

water quality parameter represents an insignificant departure from the historical condition, known as a de 

minimus change (US Sixth Circuit Court 2008). Therefore, the long-term geometric mean limit was derived 

to allow for up to a ten percent increase in the long-term geometric mean, which was calculated as the 

geometric mean of the annual geometric means of the long-term dataset for each segment of the 

waterbody.

Because it is not always practical to assess compliance with the criteria on the same long-term basis, FDEP 

also developed criteria expressed as an annual geometric mean so that estuaries could be assessed on an 

annual basis. It should be noted that the duration and frequency components of the criteria must be 

linked to the response timeframe of the sensitive endpoint. Short-term averaging periods (e.g., 1 to 30 

days) might be appropriate for nutrient criteria where a sufficiently robust cause-effect relationship has 

demonstrated that a eutrophic response occurs over such timeframes. If however, such a short-term 

response cannot be demonstrated, or there is no indication of use impairment, longer averaging periods 

should be used.

Since the duration and frequency components of the criteria must be consistent with the derivation of the 

magnitude component, the long-term geometric mean target cannot simply be applied as an annual 

mean. Doing so would result in an unacceptability high Type I failure rate (identifying a healthy system as 

being impaired) since approximately 50 percent of the individual yearly means are expected to be above 

the long-term mean. Therefore, the long-term target must be adjusted to allow for the application to a 

shorter duration with an acceptable Type I error rate of no more than a 10 percent.

An annual criterion with an approximate 10 percent Type I error rate for a given frequency was derived by 

appropriately accounting for the annual variability above the mean. This annual target concentration was 

derived as an upper percentile of the distribution of the annual geometric mean concentrations. Previous 

proposals by EPA have utilized three-year assessment periods to express the duration nutrient criteria 

components. Although it is possible to construct a test that achieves the 10 percent Type I error rate 

target over a 3-year period, a slightly longer period (5 years) will provide better control for Type II error 
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Draft 18 June 2010

and will more fully capture climatic cycles (e.g., el nino, la nina), which tend to be longer than three years 

in Florida (and may actually be on a multi-decadal scale). Furthermore, a five year period is more 

consistent with both the State’s five year 303(d) assessment and NPDES permit renewal cycles.

Given a five year assessment period, FDEP derived criteria expressed as an annual geometric mean by 

using the 75th

• As an annual geometric mean for a network of stations in a specified segment of the waterbody; and 

percentile of the annual geometric means from the long-term dataset. FDEP demonstrated 

that setting the criteria at this percentile results in a magnitude that, when expressed as an annual 

geometric mean not to be exceeded more than twice during a five-year period, will achieve the targeted 

10 percent error rate. The magnitude component of the criteria (not to be exceeded more than twice in a 

5 year period) was established to allow for two separate assessments:

• As an annual geometric mean for a single station in a given segment.

The two expressions of magnitude differ in the handling of within-segment spatial variability. The network 

average magnitude was calculated based on the distribution of spatially averaged annual geometric 

means, while the single site magnitude was calculated using the distribution of station annual geometric 

means. Use of the network average magnitude is appropriate for assessing overall segment status. 

However, a network average is only representative of overall segment status if it is relatively 

homogeneous. If the segment is not well mixed, is very large, or contains localized nutrient sources, then 

there is a potential that isolated areas of enrichment may be masked in the network spatial average.

Therefore, the single station annual geometric mean has the benefit of assessing localized enrichment 

patterns. DEP has not decided whether both expressions of magnitude are needed in all cases, and we are 

seeking additional feedback from local experts and stakeholders.

Summary of the Proposed Criteria

FDEP intends to propose three sets of potential criteria: a) a long-term geometric mean concentration; b) 

an annual geometric mean of values from a network of stations over a given area, not to be exceeded 

more than twice in a five-year period; and c) an annual geometric mean of values from a single location, 

not to be exceeded more than twice in a five-year period.

These calculations for the Nassau-St. Mary’s Estuaries have not yet been completed.
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Draft 19 June 2010

References

Baker, L. A., P. L. Brezonik, and C. R. Kratzer. 1981. Nutrient loading-trophic state relationships in Florida 

Lakes. Publ. No. 56, Water Resources Research Center, University of Florida, Gainesville, FL.

Borum, J. 1996. Shallow waters and land/sea boundaries. In Jorgensen, B. and Richardson, K., (eds.). 

Eutrophication in Coastal Marine Ecosystems. American Geophysical Union, Washington, D.C., pp. 

179-203.

CDM/DHI. 2002. Generation of a Curvilinear-orthogonal Grid and Tidal Model for the Northern Coastal 

Basin. Final Report to the St. Johns River Water Management District, Palatka, FL.

Ceric, A., Winkler, S., and E.Lowe. 2007. Status and Trends in Water Quality at the St. Johns River Water 

Management District: Trophic State Assessment. Poster. AWRA Annual Meeting, New Mexico, 

2007.

Dame, R., M. Alber, D. Allen, M. Mallin, C. Montague, A. Lewitus, A. Chalmers, R. Gardner, C. Gilman, B. 

Kjerfve, J. Pinckney, and N. Smith. 2000. Estuaries of the South Atlantic coast of North America: 

their geographical signatures. Estuaries 23: 793-819 

Dettmann, E. H, 2001. Effect of water residence time on annual export and denitrification of nitrogen in 

estuaries: A model analysis. Estuaries 24, 481-490.

Dix, N. 2010. Nutrients, Chlorophyll, and Oysters in the GTMNERR. Presentation. Northeast Florida 

Numeric Nutrient Estuary Workshop, 2010. 

Driscoll, A., C. John, F. Morris, and P. Victor. 2002. 2-D curvilinear tidal model for the Northern Coastal 

Basin, northeast Florida. AWRA Spring Specialty Conference — Coastal Water Resources, New 

Orleans, La., May 13–15, 2002.

FDEP (Florida Department of Environmental Protection). 1996. 1996 Water-Quality Assessment for the 

State of Florida, Section 305(b) Main report. Submitted to U.S. EPA in accordance with the Federal 

Clean Water Act, Section 305(b). Tallahassee, Florida.

FDEP (Florida Department of Environmental Protection). 2005. Water Quality Status Report. Tallahassee, 

FL 216pp.

Gao, X. 2009. Nutrient and Dissolved Oxygen TMDLs for the Indian River Lagoon and Banana River Lagoon, 

Florida. Department of Environmental Protection, Tallahassee, Florida.

Harwood, V. J. and D. V. Lim. 2005. Real-Time Detection of Human Pathogens in the Nassau-St Marys River

National Estuarine Research Reserve. A Final Report Submitted to the NOAA/UNH Cooperative 

Institute for Coastal and Estuarine Environmental Technology (CICEET), Durham, NH. 53pp.

Haydt, P. J. and Frazel, Inc. 2003. Northern Coastal Basin Surface Water Improvement and Management 

Plan. St. Johns River Water Management District, Palatka, FL. 99pp.

Hitchcock, G. and D. Frazel. Unpublished raw data. Studies of Karenia brevis in northeast Florida. 

Chlorophyll, primary productivity, nutrient, and oxygen samples collected. October 16, 17, 2007.

John, C., and F. Morris. 1999. 2-D finite element hydrodynamic and transport model application to 

Tolomato John, C., and F. Morris. 1999. 2-D finite element hydrodynamic and transport model 
Nutrient Criteria Technical Support Document Nassau-St Marys River Estuary

Draft 20 June 2010

application to Tolomato and Guana rivers. Second Northern Coastal Basin Estuary workshop. 

October 7–8, 1999.

Johnson, P. G., J. Muller, and B. Holub. 1998. In Holub, B. (ed.), Northern Coastal Basins Reconnaissance 

Report. Report to St. Johns River Water Management District, Palatka, Florida.

Lee, G. F., Jones, R., 1981. Application of the OECD eutrophication modeling approach to estuaries. In 

Nielson, G. J. and Cronin, L. (eds.), Estuaries and Nutrients. Humana Press, pp. 549-568.

Livingston, R.J., A. K. Prasad, X. Niu, and S. E. McGlynn. 2002. Aquatic Botany 74: 343-367.

Mao, L. T. M., Freeman, R. and C. Basci. 2007. Hydrological Watershed Model for the Northern Coastal 

Basin North Project - Intracoastal Waterway (3I), Tolomato River (9D), and Matanzas River (9C) 

Planning Units. Technical Memorandum. Department of Water Resources, St. Johns River Water 

Management District Palatka, Florida. Ponte Vedra, FL. 151pp.

McFarlin, C. R., Brewer, S. 2008. Impact of Fertilzation on a Salt Marsh Food Web in Georgia. Estuaries and 

Coasts: 31:313-325.

Miller, J.D. 2004. Status and trends of water quality in the Northern Coastal Basin.

NOAA (National Oceanic and Atmospheric Administration). 2007. Status Review of the Eastern Oyster 

(Crassostrea virginica), Report to the National Marine Fisheries Service, Northeast Regional Office, 

February 16, 2007. NOAA Tech. Memo NMFS-F/SPO-88, March 2007.

OECD (Organisation for Economic Co-operation and Development). 1982. Eutrophication of waters. 

Monitoring, assessment and control. Cooperative programme on monitoring of inland waters 

(Eutrophication control), Environment Directorate, OECD, Paris.

Phlips, E. J., N. Love, S. Badylak, P. Hansen, J. Lockwood, C. John, and R. Gleeson. 2004. A comparison of 

water quality and hydrodynamic characteristics fo the Guana tolomato Matanzas national 

Estuarine Research Reserve and the Indian River Lagoon of Florida. Journal of Coastal Research 45: 

93-109.

Phlips, E. J.; Love, N.; Badylak, S.; Hansen, P.; John, C.V., and Gleeson, R., 2004. A Comparison of Water 

Quality and Hydrodynamic Characteristics of the Nassau-St Marys River National Estuarine 

Research Reserve and the Indian River Lagoon in Florida. Journal of Coastal Research, Special Issue 

No. 45, 93-109.

Roman, C. t., N. Jaworski, F. Short, S. Findlay, and R. Warren. 2000. Estuaries of the northeastern United 

States: habitat and land use signatures. Estuaries 23: 743-764.

Rutledge, A. T. 1985. Ground-water hydrology of Volusia County, Florida, with emphasis on occurrence 

and movement of brackish water. U.S. Geological Survey, Water-Resources Investigations Report 

84-4206, Denver, Colorado. 

Scholl, J. E., J. Heaney, and W. Huber. 1980. Water quality analysis of the Nassau-St Marys River, Florida. 

Water Res. Bull., AWRA 16: 285-293.

Sheng, Y. P., B. Tutak, J. Davis, and V. Paramygin. 2008. Circulation and flushing in the lagoonal system of 

the Guana Tolomato Matanzas National Estuarine Research Reserve (GTMNERR), Florida. Journal 

of Coastal Research. 55: 9-25.
Nutrient Criteria Technical Support Document Nassau-St Marys River Estuary

Draft 21 June 2010

SJRWMD (St. Johns R. Water Management District). 2006. Resources map file of Northern Coastal Basins, 

Coastal Basins Section, Div. of Environmental Sciences, Palatka, Florida.

SJRWMD. 2006. Watershed Facts: Integrating environmental science and computer mapping technology. 

Accessed at the SJRWMD Web site at http://www.sjrwmd.com/archydro/factsindex.html. Based 

on data retrieved on August 17, 2006. 

Smith, V. H. 1998. Cultural eutrophication of inland, estuarine, and coastalwaters, p. 7 – 49. In M. L. Pace 

and P. M. Groffman (eds.), Successes, limitations, and frontiers in ecosystem science. SpringerVerlag.

Steward, J. S. and Lowe, E. F., 2010. General empirical models for estimating nutrient load limits for 

Florida’s estuaries and inland waters. Limnol. Oceanogr. 55, 433-445.

Steward, J. S., W. C. Green, and J. D. Miller. 2010a. Using multiple lines of evidence for developing numeric 

nutrient criteria for Tolomato-Matanzas Estuary, Florida. Draft SJRWMD report to FDEP, 

Tallahassee, Florida.

Steward, J. S., W. C. Green, and J. D. Miller. 2010b. Using multiple lines of evidence for developing numeric 

nutrient criteria for Halifax River Estuary, Florida. Draft SJRWMD report to FDEP, Tallahassee, 

Florida.