Nutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 1 June 2010 

# Site Specific Information i n 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, 2010Nutrient 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 Sourc es and Studies

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

................................ ................................ ................................ ................................ ..... 13

Numeric Nutrient Criteria Recommendation

................................ ................................ ................................ .. 14

References

................................ ................................ ................................ ................................ ..................... 19Nutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 3 June 2010 

### 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
, i ncluding surrounding urban areas, dischar gers, 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 impro ved from Steward and Lowe (2010) 15Nutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

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 t he 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 n utrient 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 sh ows 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. M arys 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 I sland
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 Talb ot 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 shoreli ne erosion, septic tanks and wastewater treatment facilitie s.Nutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 5 June 2010 Oyster reefs and salt marshes are the primary aquatic resource s 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

.Nutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 6 June 2010 Table 1 . Checklist of nutrient enrichment symptoms in the Nassau

- St Marys Estuary

Response V ariable Observed historically? Observed currently? Explanation

Low DO (hypoxia/anoxia) No Yes N aturally 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. Natu rally occurring high turbidity and color (blackwater river) contributes to reduced water clarity. Increased chlorophyll a concentrations Yes Yes NOAA (1996) and DeVivo (2009) reported leve ls of chlorophyll

- a: >5, <20 which is consistent with current values. W etlands 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, n aturally high turbidities

, and highly colored water may have prevent ed 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 fl at and low near the Atlantic coast and rises inland to the Duval Uplands, Trail Ridge, and Northern Highlands . The coastal lowlands are poorly
draine d 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 are as. 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

we ather by wastewater effluent withdrawn originally from the Floridan aquifer through wells. The lowerNutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 7 June 2010 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 whe n 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

se ason, 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 poo rly 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. Scatter ed 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 surfa ce 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 managemen t of

wa ter 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. Jo hns 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 bo undary 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 fl ow of about 1,400 cubic feet per second (cfs) at its mouth (Georgia Departme nt 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

wet lands 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
i nfl uenced 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.Nutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 8 June 2010 The major environmental stressors include oxygen

- demanding substances

, bacter ial 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 munic ipal 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 di strict 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 subu rban 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 subare a 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 t ributaries in the Middle St. Marys are short and originate on the Trail Ridge. The Suwannee Canal is located in this subarea, fl owing
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 ha ve measured tidal inf l uences 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 limite d development in much
of the lower St. Marys River, primarily due to the lack of soil suitability for septic systems in the fl oodplain 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.Nutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 9 June 2010 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 betwee n 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 b e 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 upst ream 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 Wildli fe 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 p hysical /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 fresh water residence time 2

- 29 days Scavia and Liu (2009)
Watershed Land Use (2004) Water/ Wetland 2 1

. 3 1% SJRWMD 2000 Range/ Forest 39. 1 % SJRWMD 2000

Urban 2.47 SJRWMD 2000 Agriculture 2.61 SJRWMD 2000 Unknown (no data) 25.7 SJRWMD 2000Nutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 10 June 2010 

### Sources of Nutrients

Potential n onpoint 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 oth er 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 inadequ ately 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 fl ow gre ater than one million gallons per day (mgd). There ar e also six minor discharges (fl ow less than one mgd). Additionally, there are relatively few industrial wastewater discharges, including one major facility (GDNR, 2002).

Within Florida, there are a numbe r 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 Wastewate r 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 NPDES

permitted facilities in the L ower 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 pl anning unit. It is located in Baldwin within Duval County.

There are two active landfi lls in the Georgia portion of the St. Marys Basin but no active landfills in the Florida portion of the basin. There are seven cl osed landfills (one Class I, fi ve Class II, and one Construction/ Demolition site) in the Upper St. Marys River planning unit, and one closed landfill (Cl ass II)
and one inactive landfi ll (Class III) in the MiddleSt. Marys River planning unit.


### Biological Summary

The biological communities that c haracterize the vast majority of the aquatic habitat in the Nassau

- St Marys River Estuary are tidal marshes and oyster reefs (Steward 2010)

. W ater quality data suggest that maintaining current nutrient loads will achieve a chlorophyll

- based light transpare ncy 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 dyn amic 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 sapidu s ), and amphipods.Nutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 11 June 2010 Figure 2: St. Marys Estuary , i

ncluding 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 suggesti ng 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 unpub lished presentation, 2010).

Salt Marsh

Salt marshes are a nother common commu nity type in the HRE

. D ominant plants include saltmarsh cordgrass ( Spartina alterniflora ), black needlerush ( Juncus roemerianus ), Glasswort ( Salicornia spp.), andNutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 12 June 2010 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, v ariation 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 t o have a stimulatory effect on plants and herbivores.

Plankton
Livingston (2002) conducted a n 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 o f 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 we re 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 cou ld 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 phytopl ankton 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 th e 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, t hese 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 E nvironmental Protection (FDEP)

,

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

**•** City of Jacksonvi lle/Duval County,

**•** National Park Service (NPS),

**•** Georgia Environmental Protection Division (GEPD) ( mainstem of St. Marys River only)Nutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 13 June 2010 

### Waters on 303(d) List

According to the Geor gia 2000 305(b)/303(d) list, fi ve 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 prima ry 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 fi sh consumption and DO (GDNR, 2002).

The most common parameters listed for impa irment 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 flo w 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 a re 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 th at 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 b lackwater 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 ThresholdsNutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 14 June 2010 

### 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 75 th and 90 th percentile of the data.

Figure 3. Annual geometric mean for total nitrogen, 1980

- 2004.

Figure 4. Annual geometric mean for total phosphorus, 1971

- 2004.Nutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 15 June 2010 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 amon g analytes) . LN = natural logarithm, GM = geometric mean, C.I. = confidence interval. Long term geometric means and the 90 th

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 w as 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 r esults (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, t he 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/m 2 /yr) vs. hydraulic loa ding (q s ) 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 m estrophic 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 withou t 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 ca use

- 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 crite rion 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 an d 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 referenceNutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 17 June 2010 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 brief ly 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 valu es 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 t he 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 T ype 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 lon g

- 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 crit eria 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 resul t 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 t o 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 d uration 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 errorNutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 18 June 2010 and will more f ully 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 75 th

**•** 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 cr iteria 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 t o 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 m agnitude was calculated using the distribution of station annual geometric

means. Use of the network average magnitude is appropriate for assessin g 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 a nnual 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.Nutrient Criteria Technical Support Document Nassau

- St Marys River Estuary

Draft 19 June 2010 

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