Site-Specific Information 

in Support of 

Establishing Numeric Nutrient 

Criteria for the Florida Keys

Florida Department of Environmental Protection

Tallahassee, FL 32399

August 18, 2010
Nutrient Criteria Technical Support Document Florida Keys

Draft ii August 2010

Table of Contents

Executive Summary............................................................................................................................1

Geographic and Physical Description ..................................................................................................5

Sources and Fates of Nutrients...........................................................................................................7

Nutrient Sources and Loading Estimates.................................................................................................. 7

Biological Summary .........................................................................................................................13

Seagrasses...............................................................................................................................................13

Coral Reefs ..............................................................................................................................................19

Additional Biological Resources..............................................................................................................25

Water Quality Studies......................................................................................................................27

Waters on the 303(d) List.................................................................................................................33

Numeric Nutrient Criteria Recommendations ...................................................................................37

FKRAD recommendations .......................................................................................................................38

FDEP Nutrient Criteria Approach ............................................................................................................40

Proposed Numeric Nutrient Criteria........................................................................................................43

Comparison of FKRAD and FDEP approaches .........................................................................................47

References.......................................................................................................................................50

Appendix A. Permitted facilities and landfills in the Florida Keys basin by planning unit (FDEP 2008b).

........................................................................................................................................................54
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List of Tables

Table 1. Checklist of nutrient enrichment symptoms in the Florida Keys. ................................................... 3

Table 2. State parks and aquatic preserves. ................................................................................................ 6

Table 3. Estimated annual nutrient loadings in 1999 (lbs year-1) for the different Keys regions 

(FDEP 2008a). ............................................................................................................................. 8

Table 4. Comparison of total 1999 estimated annual anthropogenic land based (wastewater and 

stormwater) nutrient loadings to the Keys (FDEP 2008a) with some estimated farfield 

loadings from Florida Bay passes and Atlantic upwelling (Gibson et al. 2008) and 

atmospheric deposition (calculated using atmospheric loading estimates in Rudnick et 

al. 1999) in metric tons year-1. ................................................................................................. 13

Table 5. Catch statistics for the 15 more abundant reef fish species observed during the Florida 

Keys visual sampling, 1999–2006.............................................................................................26

Table 6. Water quality variables measured in the FKNMS, March 1995–December 2008 (Boyer 

and Briceño 2009).....................................................................................................................30

Table 7. Verified impairments in the Florida Keys basin. ............................................................................34

Table 8. Natural background conditions (modeled) and water quality targets for the northern 

Keys (FDEP 2008a). ...................................................................................................................38

Table 9. Natural background conditions (modeled) and water quality targets for the central Keys 

(FDEP 2008a). ...........................................................................................................................38

Table 10. Natural background conditions (modeled) and water quality targets for the southcentral Keys (FDEP 2008a)........................................................................................................39

Table 11. Natural background conditions (modeled) and water quality targets for the southern 

Keys (FDEP 2008a). ...................................................................................................................39

Table 12. 1985 FDEP OFW water quality data (FDEP 2008a). ....................................................................40

Table 13. Range and means of modeled TN and TP targets for bayside and oceanside bubble 

WBIDs (FKRAD 2008). ...............................................................................................................40

Table 14. Proposed regionalization for the Florida Keys............................................................................41

Table 15. Proposed numeric nutrient criteria for all segments of the Florida Keys, including TP, 

TN, and chlorophyll a. For compliance purposes, the long term geometric mean shall 

not exceed the long term limit nor shall the average of all stations in a segment 

exceed the network average more than twice in a 5 year period. The last column 

shows the value which single station shall not exceed, by segment, more than twice in 

a 5 year period..........................................................................................................................46

Table 16. Comparison of TN (μg l-1) targets for halo zone modeled WBIDs and OFW targets (from 

the FKRAD) with nearshore FDEP criteria proposed for sub-basins using FIU long-term 

water quality data. For maps showing the locations of WBIDs and sub-basins, see 

Figures 24 and 25......................................................................................................................48

Table 17. Comparison of TP (μg l-1) targets for halo zone modeled WBIDs and OFW targets (from 

the FKRAD) with nearshore criteria proposed for sub-basins using FIU long-term 

water quality data. For maps showing the locations of WBIDs and sub-basins, see 

Figures 24 and 25......................................................................................................................49
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List of Figures

Figure 1. Map of the Florida Keys and FKNMS boundary. ........................................................................... 5

Figure 2. Regional circulation patterns in the Florida Keys (Lee et al. 2007)............................................... 7

Figure 3. Nitrogen loading to Florida Bay and the Florida Keys (Gibson et al. 2008; Key for 

sources in figure: a. Gibson et al. 2008, b. Boyer and Keller 2007, c. Rudnick et al. 

1999, d. Kruczynski and McMannus 2002, e. Leichter et al. 2003)...........................................11

Figure 4. Phosphorus loading to Florida Bay and the Florida Keys (Gibson et al. 2008; Key for 

sources in figure: a. Gibson et al. 2008, b. Boyer and Keller 2007, c. Rudnick et al. 

1999, d. Kruczynski and McMannus 2002, e. Leichter et al. 2003)...........................................12

Figure 5. Conceptual model of the relationship between seagrass leaf nutrient content and 

nutrient availability in south Florida (Fourqurean and Rutten 2003).......................................15

Figure 6. Conceptual model relating nutrient availability (trophic state) to the abundance of 

primary producers in nearshore marine waters of south Florida (Fourqurean and 

Rutten 2003). ............................................................................................................................16

Figure 7. EI status of seagrasses in the FKNMS for 2006, 2007, and 2008 compared with the 

long-term mean EI (dashed line) for 1995 to 2005 (Fourqurean and Escorcia 2009)...............17

Figure 8. SCI status of seagrasses in the FKNMS for 2006, 2007, and 2008 compared with the 

long-term mean SCI (dashed line) for 1995 to 2005 (Fourqurean and Escorcia 2009).............17

Figure 9. Seasonality of epiphyte load, averaged across all 30 Level 1 sites, 2001–09 (Fourqurean 

et al., in press)...........................................................................................................................18

Figure 10. Line graph of mean annual percent cover for the four major benthic taxa recorded in 

CREMP image analysis (CREMP 2010). Mean percent cover is pooled from 97 stations 

in the Florida Keys.....................................................................................................................20

Figure 11. Line graph of the mean annual percent cover for six species of stony corals. Mean 

percent cover is pooled from 97 stations (CREMP 2010)..........................................................21

Figure 12. Long term trends of percent cover from 1999-2008 at CREMP sites for a) stony corals 

and b) octocorals (CREMP 2010). .............................................................................................22

Figure 13. Number of stations with stony coral disease recorded (Callahan et al. 2007). ........................23

Figure 14. Percent cover comparisons between summer 2009 and February 2010 for a) stony 

corals and b) octocorals at eight stations (CREMP 2010).........................................................24

Figure 15. Mean fish density by year (2000–06) as recorded during visual surveys in the Florida 

Keys (Donahue et al. 2008).......................................................................................................26

Figure 16. Map of study area (Boyer 2010). ..............................................................................................28

Figure 17. Florida International University (FIU) Southeast Environmental Research Center 

(SERC) Water Quality Monitoring Network. Stations in red are sampled as part of the 

FKNMS monitoring program (Boyer and Briceño 2009). ..........................................................29

Figure 18. Median salinity, 1995–2009 (Boyer and Briceño 2009). ...........................................................31

Figure 19. Dissolved inorganic nitrogen (micromolar[μM]) median, 1995–2007 (Boyer and 

Briceño 2009)............................................................................................................................31

Figure 20. TP (μM) median, 1995–2007 (Boyer and Briceño 2009)...........................................................32

Figure 21. Chlorophyll a (μg L-1) median, 1995–2007 (Boyer and Briceño 2009).......................................32

Figure 22. Dissolved inorganic nitrogen (μM) (Boyer and Briceño 2009). .................................................33
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Figure 23. Map of the Florida Keys with WBIDS and regions (north, central, southcentral, and 

southern) identified (FDEP 2008a)............................................................................................36

Figure 24. WBID models in the Florida Keys (McClelland 2010). ...............................................................37

Figure 25. Proposed estuarine and coastal nutrient criteria sub-basins for South Florida........................42
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Executive Summary

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

with the U.S. Environmental Protection Agency (EPA) and local scientists, to support the development of 

numeric nutrient criteria for the Florida Keys. 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. This report presents approaches for setting criteria for the Florida Keys in 

both the halo zone (within 500 meters [m] from shore) and nearshore zone waters (state waters beyond 

500 m). 

The Florida Keys are an archipelago of islands in Monroe County, Florida, that extend from the southern 

tip of Florida over 354 kilometers (km) to the southwest (Collado-Vides et al. 2007; Figure 1). Consisting 

of 822 islands, of which about 30 are inhabited, the Keys are traversed by U.S. Highway 1 (also known as 

U.S. 1 or Overseas Highway) with 19 miles of bridges (FDEP 2008). The Florida Keys National Marine 

Sanctuary (FKNMS), consisting of 9,500 square kilometers (km2

) of coastal and oceanic waters and 

submerged lands that surround the entire Florida Keys island chain, was established in 1990 (Figure 1). 

The Keys are generally divided into three geographic areas: the Upper, Middle, and Lower Keys (Figure 

2). The three regions are further divided into oceanside and bayside. The bayside regions of the Lower 

and Middle Keys are known as Backcountry and Sluiceway, respectively. 

There are both anthropogenic and natural sources of local and external nutrient loads to the Keys. The 

Florida Keys are directly influenced by the Florida Current, the Gulf of Mexico Loop Current, inshore 

currents of the Southwest Florida Shelf (Shelf), discharge from the Everglades through Shark River 

Slough, and tidal exchange with both Florida Bay and Biscayne Bay (Lee et al. 2002). FDEP recognizes 

that there are land-based sources of nutrients in the Keys, such as wastewater and stormwater, which 

may contribute to the nutrient regime in waters of the Keys. The Florida Keys Reasonable Assurance 

Document (FKRAD) (FDEP 2008) identified local nutrient sources in the Keys, including wastewater and 

stormwater originating from unincorporated Monroe County in the Key Largo area; the Villages of 

Islamorada, Marathon, Key Colony Beach, and Layton; the City of Key West; the Florida Department of 

Transportation (FDOT); and the Florida State Park Service. Additionally, in the south-central and 

southern Keys, stormwater and wastewater originate from the U.S. Navy facilities in Boca Chico and 

those adjacent to the City of Key West.

The three dominant habitats that make up the coastal marine ecosystems of the Florida Keys are 

seagrass meadows, coral reefs, and mangroves. Seagrasses are the principal component of benthic 

marine habitats in the Keys, occupying over 70% of the FKNMS (Fourqurean et al. 2003). Coral reefs, 

patch reefs, and hardbottom habitats cover approximately 7%, 1%, and 19% of the FKNMS, respectively. 

Mangroves are a dominant feature of the land-sea margin throughout the Florida Keys.

Long-term monitoring of water quality indicates that nitrate and total organic carbon (TOC) follow a 

concentration gradient, with higher levels in the nearshore area and declining concentrations away from 

shore, implying a land-based source (Boyer and Briceño 2009). However, neither total phosphorus (TP) 

nor chlorophyll a concentrations show a trend with distance from land. The Keys are an extremely
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oligotrophic system and anthropogenic nutrient loads may not be immediately observed in the water 

column due to rapid assimilation by seagrasses and other benthic flora. 

Florida Keys waters were listed as impaired for nutrients on the 1998 303(d) list. However, as provided 

for in the Impaired Surface Waters Rule (Chapter 62-303, Florida Administrative Code [F.A.C.]), the Keys 

have not been placed on the verified list of impaired waters because local stakeholders provided 

documentation that nutrient loads from local sources will be reduced as part of a Keys restoration 

process (see the Florida Keys Reasonable Assurance Document [FKRAD] (FDEP 2008a)). 

For the purposes of nutrient criteria development, FDEP has considered the halo zone (within 500 m) 

and nearshore zone (state waters beyond 500 m) areas of the Florida Keys separately and is applying 

two different approaches for establishing numeric nutrient criteria. 

For the halo zone area, FDEP has yet to develop numeric nutrient criteria, but plans to apply a “response 

based” approach that is based on the FKRAD document. As indicated in the FKRAD, existing canal 

nutrient levels and loading from land based sources of nutrients may contribute to the designated uses 

not being supported in the canals (in addition to physical constraints). The FKRAD was developed to set 

forth and accelerate actions that have been taken or are planned to be taken to reduce nutrient 

loadings throughout the Florida Keys so that water quality standards are met and beneficial uses are 

restored (FDEP 2008a). The FKRAD is based on improving water quality to targets developed using a 

land-use model. The water quality targets would be assessed at the boundary of the halo zone, which is 

defined as 500 m from shore. Although the FKRAD does not specifically address criteria for canals, FDEP 

supports the outlined load reductions in order to improve water quality at 500 m and help ensure that 

criteria are met in nearshore waters. The FKRAD targets for the halo zone boundary are presented in 

Tables 8-11 in this report.

For the nearshore waters, FDEP is applying a “maintain existing healthy conditions” approach. FDEP’s 

evaluation of the biological resources indicates that the waters support a healthy well-balanced 

community, are attaining the designated use, and have not shown adverse effects from nutrient 

enrichment in the nearshore area. Although there have been changes in some communities (e.g., coral 

loss) (Table 1), evidence suggests that causes other than nutrients are responsible for the responses. 

Waters in the nearshore area will be subdivided into segments of similar water quality and criteria

established to maintain the current nutrient data distributions, which would continue to support the

existing healthy condition. These criteria are presented in Table 15 in this report. 
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Table 1. Checklist of nutrient enrichment symptoms in the Florida Keys. 

- = Empty cell/no data

Response variable Observed 

historically

or 

currently? 

Explanation Source

Low dissolved 

oxygen (DO) 

(hypoxia/anoxia)

Yes Low DO concentrations have been observed in canals in the Keys and were 

observed at several nearshore stations during sampling in 1985 for the OFW 

designation. Diel low DO in SAV beds is a natural phenomenon resulting from 

SAV respiration.

FDEP (2008)

Reduced clarity Yes There has been increased turbidity in nearshore areas, likely due to resuspension 

of sediments by wind and wave action. However, light penetration to SAV beds 

generally exceeds 40% of surface values, meaning light is not a limiting factor for 

SAV growth throughout the Keys. 

Boyer and 

Jones (2002)

Increased 

chlorophyll a

concentrations

No Chlorophyll a has not increased over time nor does it vary as a function of 

distance from land. Chlorophyll a median concentrations are extremely low (0.19 

micrograms per liter [μg l-1]) for the monitoring period between 1995 and 2008. 

Boyer and 

Briceño 

(2009) 

Phytoplankton 

blooms (nuisance 

or toxic)

Yes Periodic algae blooms originate on the Gulf side of the Keys in Florida Bay or 

along the southwest Shelf, and are not associated with human activities. The 

Blackwater event in 2002, resulting from natural tannic inputs into west Florida 

coastal waters, included a nontoxic algal bloom that was carried south through 

the Keys. More recently, in 2005 and 2006, blooms associated with highway 

development and hurricane activity were restricted to Barnes Sound and Lake 

Surprise. 

- 

Problematic 

epiphyte growth 

No Epiphyte growth is highly seasonal, and recent experimental studies have not 

found increased epiphytes associated with nutrient additions due to the activity 

of grazers.

e.g., 

Fourqurean et 

al. (in press)

Problematic 

macroalgal growth

No Abundance of calcareous macroalgae in the FKNMS has increased over time, 

however, calcareous macroalgae is considered a viable benthic habitat. Sites 

closest to land and with the highest water column nitrogen (N) concentrations 

have the highest calcareous algae abundance. 

e.g. Lapointe 

et al. (2004), 

Collado-Vides 

et al. (2005) 

and (2007), 

Fourqurean et 

al. (in press)

Submerged 

aquatic vegetation 

(SAV) community 

changes or loss

No Data from the FKNMS monitoring program’s permanent stations indicate no

significant sanctuary-wide decrease in SAV coverage or adverse changes in 

community composition and show no clear spatial pattern that human activities 

have resulted in adverse eutrophication effects. Monitoring results indicate that 

there are early signs of eutrophication within the 500 m halo zone, but those 

eutrophication effects have not manifested themselves to where there is 

imbalance of flora and therefore have not exceeded the narrative criteria. 

Thalassia tissue nitrogen:phosphorus (N:P) ratios are being investigated to 

determine if this metric may be indicative of early signs of eutrophication. 

e.g., 

Fourqurean 

and Escorcia 

(2009) 

Emergent or 

shoreline 

vegetation 

community 

changes or loss 

Yes Shoreline vegetation has changed in many areas where human development has 

occurred due to physical (not nutrient) disturbance. 

- 

Coral/hardbottom 

community 

changes or loss 

Yes Coral cover has significantly declined, and there have been periodic outbreaks of 

coral diseases (black band and other diseases) in the Keys and throughout the 

Caribbean. Overall mean percent stony coral cover has been stable since 1999. 

Changes in coral health (cover and condition) has not been directly related to 

anthropogenic land-based sources of nutrients.

Donahue et 

al. (2008), 

Callahan et al. 

(2007) 

LIrman and 

Fong (2007)
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Impacts to benthic 

community 

- Covered above. - 

Fish kills Yes Periodic fish kills have been attributed to factors other than nutrient enrichment 

(e.g., low DO, red tide, cold, and other factors). 

Florida Fish 

and Wildlife 

Research 

Institute 

(FWRI) 
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Geographic and Physical Description

The Florida Keys are an archipelago of islands in Monroe County, Florida, that extend from the southern 

tip of Florida over 354 km to the southwest (Collado-Vides et al. 2007; Figure 1). About 30 of the 822 

islands are inhabited and the Keys are traversed by U.S. Highway 1 with 19 miles of bridges (FDEP 2008). 

Approximately 34% of the land area in the Keys portion of Monroe County is conserved (Monroe 

County 2010). 

The Florida Keys was designated an Outstanding Florida Water (OFW) in 1985, and in 1990, the the 

entire Florida Keys island chain and the 9,500 km2 of coastal and oceanic waters and submerged lands 

that surround it were established as the Florida Keys National Marine Sanctuary (Figure 1). The Keys are 

bordered to the north and northwest by Biscayne National Park and Everglades National Park. There are 

also 2 aquatic preserves and 10 state parks located in the Keys (Table 2). 

The Florida Keys region is underlain by the extremely permeable Key Largo Formation limestone, and 

the Keys have little vertical relief (5 meter maximum at Windley Key). Soils quickly infiltrate runoff and 

its pollutants are transported rapidly to nearshore waters with little or no nutrient entrapment in the 

soil matrix (FDEP 2008). The islands function as a discontinuous, semipermeable dam that separates 

Florida Bay from the Atlantic Ocean (Reich et al. 2002). 

The Keys are generally divided into three geographic areas: the Upper, Middle, and Lower Keys (Figure 

2). The Lower Keys are most influenced by cyclonic gyres that spin off the Florida Current, the Middle 

Keys by exchange with Florida Bay, and the Upper Keys by Florida Current frontal eddies and somewhat 

by exchange with Biscayne Bay (Figure 2; Boyer and Briceño 2008). The three regions are further 

divided into oceanside and bayside. The bayside regions of the Lower and Middle Keys are known as 

Backcountry and Sluiceway, respectively. 

Figure 1. Map of the Florida Keys and FKNMS boundary.
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Table 2. State parks and aquatic preserves.

Name Description

Coupon Bight Aquatic 

Preserve

• 4,600 acres of seagrass meadows, hard bottom communities, mangrove 

wetlands, and coral reefs

• The patch reef community includes sponges, soft and hard corals, and algae

• Home to rare wading birds and the endangered Key deer

Lignumvitae Key Aquatic 

Preserve

• 7,000 acres of seagrass meadows, deep water channels, hard-bottom 

communities and mangrove wetlands

• Lignumvitae Key Botanical State Park overlaps with much of the preserve

Dagny Johnson Key Largo 

Hammock Botanical State 

Park

• Contains one of the largest tracts of West Indian tropical hardwood 

hammock in the United States

• Home to 84 protected species of plants and animals

John Pennekamp Coral 

Reef State Park

• First underwater park in the United States 

• 70 nautical square miles with coral reefs and associated marine life

• Upland area includes mangrove swamps and tropical hammocks

Windley Key Fossil Reef

Geological State Park

• Formed of Key Largo limestone, fossilized coral

• Historically was a quarry used for stone to build the Flagler Railroad

Indian Key Historic State 

Park

• Tiny island accessible only by canoe or kayak

San Pedro Underwater 

Archaeological Preserve 

State Park

• Underwater archeological preserve that features a submerged shipwreck

Lignumvitae Key

Botanical State Park

• Virgin tropical hardwood hammock only accessible by boat

Long Key State Park • Profusion of plant and animal life

• Known for bonefishing

Curry Hammock State 

Park

• Group of islands

• Hardwood hammocks support a large population of thatch pines

• Other communities include mangrove swamps, seagrass beds, and wetlands

Bahia Honda State Park • Site of hawksbill turtle nesting

Fort Zachary Taylor

Historic State Park

• Fort was constructed in the mid-1800s to defend the nation’s southern

coastline
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Figure 2. Regional circulation patterns in the Florida Keys (Lee et al. 2007).

Sources and Fates of Nutrients

Nutrient Sources and Loading Estimates

The water quality of the FKNMS can be directly affected both by local nutrient loading sources and 

external nutrient transport (Boyer and Briceño 2009). There are both anthropogenic and natural 

sources for the local and external nutrient loads. The FKNMS is directly influenced by the Florida 

Current, the Gulf of Mexico Loop Current, inshore currents of the Shelf, discharge from the Everglades 

through Shark River Slough, and tidal exchange with both Florida Bay and Biscayne Bay (Lee et al. 2002). 

Advection from these external sources significantly affects the physical, chemical, and biological 

composition of waters within the FKNMS, as does internal nutrient loading and freshwater runoff from 

the Keys themselves (Boyer and Jones 2002). 

Local anthropogenic nutrient sources within the Keys include point source discharges (domestic 

wastewater) and nonpoint source inputs, such as septic tanks and stormwater. The FKRAD (FDEP 2008a) 

identified local nutrient sources in the Keys, including wastewater and stormwater originating in 

unincorporated Monroe County in the Key Largo area; the Villages of Islamorada, Marathon, Key Colony 

Beach, and Layton; the City of Key West; the Florida Department of Transportation (FDOT); and the 

Florida State Park Service. Additionally, in the south-central and southern Keys, stormwater and 

wastewater originate in the U.S. Navy facilities both in Boca Chico and those adjacent to the City of Key 
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West. Table 3 provides a summary of the estimated contribution of nutrients from wastewater and 

stormwater to WBIDS in the north, central, south-central, and southern regions of the Keys for the 

baseline time period of 1999. Load estimates were calculated as part of the Florida Keys Carrying 

Capacity Study based on the number of equivalent dwelling units (EDUs), their estimated daily flows and 

the effluent characteristics of their wastewater treatment methods. Table 4 provides load estimate 

totals by regions converted to metric tons per year (m tons year-1) for comparison with estimates of 

farfield nutrient sources.

The 2008 Water Quality Assessment Report for the Florida Keys provides the following information on 

permitted discharges within each planning unit (FDEP 2008b; a full list of discharging facilities is 

provided in Appendix A). In the Upper Keys planning unit there are 147 permitted wastewater facilities, 

of which 139 are domestic waste facilities, five are industrial waste facilities, two are industrial 

stormwater discharges, and one is an underground injection control facility. Of these facilities, only two

discharge to state surface waters, and those are the stormwater discharges. There are 91 permitted 

wastewater facilities in the Middle Keys planning unit, of which 83 are domestic waste facilities, six are 

industrial waste facilities, and two are industrial stormwater discharges. Of these facilities, two

discharge to state surface waters, and those are the stormwater discharges. There are 57 permitted 

wastewater facilities in the Lower Keys Planning Unit, of which 51 are domestic waste facilities, five are 

industrial waste facilities, and one is an industrial stormwater discharge. Three of these facilities 

discharge to state surface waters: one domestic waste facility, one industrial waste facility, and one 

stormwater discharge. There are two inactive solid waste landfills in the Upper Keys planning unit, in 

the Middle Keys there are two solid waste landfills, one active and one inactive; and in the Lower Keys 

there are four landfills, two active and two inactive; however, the solid waste is currently sent to the 

mainland for disposal. There are no hazardous waste sites, Superfund sites, state-funded waste 

cleanup sites, or delineated ground water contamination areas in the Upper Keys, Middle Keys, or Lower 

Keys Planning Units. 

Table 3. Estimated annual nutrient loadings in 1999 (lbs year-1) for the different Keys regions (FDEP 2008a). 

WBID Wastewater Stormwater

TN TP TN TP

Northern

6006A-N 66,869 19,324 21,469 3,310

6006A-S 67,601 19,643 28,338 4,442

6006B-N 585 167 19,985 3,257

6006B-S 1,847 497 4,489 721

6006C-N 12,488 3,747 4,477 748

6006C-S 6,522 1,956 5,247 810

6009-N 30,541 8,829 8,988 1,288

6009-S 23,975 6,899 4,557 634

6017-N 12,643 3,709 3,035 423

6017-S 16,149 4,823 3,058 398

6019-N 7,920 2,315 3,496 574
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6019-S 4,462 1,413 1,402 227

Northern - 

Total

251,573 73,346 108,842 16,832

Central

6010-N 5,180 1,546 1,740 251.18

6010-S 1,357 407 2,935 462.49

6011A-N 5,180 1,546 1,740 251.18

6011A-S 1,357 407 2,935 462.49

6011B-S 38,089 9,665 9,433 1,502.94

6011C-N 9,043 2,688 2,514 385.03

6011C-S 4,146 1,200 1,558 238.10

6016-N 802 233 142 20.30

6016-S 7,492 2,248 1,958 281.17

Central - Total 129,856 35,288 34,848 5,529

Southcentral

6012A 30,009 8,943 21,362 3,353

6012C 193 58 2,842 460

6012D 346 104 1,280 205

6012E 1,175 343 3,113 511

6013A 11,971 3,558 22,724 3,806

6013B 632 188 843 132

6013C 28,183 8,162 15,223 2,449

6013D 82 25 787 128

6014C 25,498 7,532 23,910 4,566

6018 2,388 716 3,085 480

Southcentral - 

Total

100,477 29,629 95,169 15,650

Southern

6014A-N 114,276 34,283 12,491 1,730

6014A-S 62,651 18,797 10,516 1,603

6014B-N 9,191 2,754 3,289 474

6014B-S 23,100 8,775 4,349 619

Southern - 

Total

209,218 64,609 30,645 4,427

Submarine ground water discharge is also a component of nutrient input in the Keys (Lapointe et al. 

1990, Lapointe and Matzie 1996). Lapointe et al. (1990) assessed the degree of nutrient enrichment of 

limestone ground waters by onsite sewage disposal systems (septic tanks) and evaluated seasonal 

relationships between nutrient-enriched ground waters and adjacent surface waters. They observed 

that ground waters associated with septic tanks had elevated nutrient concentrations compared with 

controls. 

Reich et al. (2002) verified the natural gradient flow of ground water from Florida Bay beneath Key Largo 

and ultimately into the Atlantic Ocean using multi-depth wells and the injection of fluorescein and 
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rhodamine dyes as tracers. The study included clusters of deep (13.6 m) and shallow (6.1 m) wells on 

the bayside and oceanside of an undeveloped area of Key Largo. They observed that the greatest 

forcing factor in ground water movement is the difference in water level between Florida Bay and the 

Atlantic Ocean. For over 6 months, Florida Bay was on average 12 to 15 centimeters (cm) higher than 

the Atlantic side. There was both horizontal and vertical flow of ground water, with the predominant 

direction of horizontal flow to the southeast, towards the reef tract. Their results indicate that a 

component of vertical flow likely contributes ground water seepage up into overlying surface waters and 

could transport nutrients and pollutants into nearshore waters as well as to the reef tract.

External sources of nutrients to the Keys include the natural and regulated discharges from the 

Everglades to Florida Bay, regulated discharges from Lake Okeechobee through the Peace River, 

Caloosahatchee River and Mississippi River discharges to the Gulf of Mexico, Atlantic upwelling, and 

atmospheric deposition (FDEP 2008a; Lapointe et al. 2004). 

Lapointe et al. (2004) quantified the role of physical forcing and water management in south Florida on 

nutrient enrichment and blooms of phytoplankton, macroalgae, and seagrass epiphytes in the Keys. 

Results suggested that regional-scale agricultural runoff (from the mainland Everglades watersheds) and 

local sewage discharges from the Keys are both significant N sources. However, Gibson et al. (2008) 

determined that while the Middle Keys passes were a significant outflow from Florida Bay towards the 

reef tract, inputs of cool, nutrient rich waters via offshore tidal bores contributed far greater amounts of 

biologically available N directly to the reef system. For P, fluxes across the open western boundary of 

Florida Bay and input from tidal bores are also important nutrient sources to the reef system. Gibson et 

al. (2008) quantified the exchange of water and nutrients through Long Key Channel using long-term, 

high-resolution, mass flow measurements, combined with periodic tidal-scale observations of nutrient 

concentrations. Loads were compared with other published values of regional nutrient loads and fluxes 

(Figures 3 and 4). 
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Figure 3. Nitrogen loading to Florida Bay and the Florida Keys (Gibson et al. 2008; Key for sources in figure: a. 

Gibson et al. 2008, b. Boyer and Keller 2007, c. Rudnick et al. 1999, d. Kruczynski and McMannus 2002, e. 

Leichter et al. 2003).

5190 

NO3-

13000

250

1240 710

5500

500

640

~2000 km

2

8800

TN Inputs and Outputs

(Metric Tons/year)

5190 ( e )

NO3

 -

“13000” ( c )

250 ( b )

“710” ( c ) 1240 ( b )

 3500 ( b )

5500 ( a )

500 ( d )

 “640” ( c )

“8800” ( b )

TN Inputs and Outputs

(Metric Tons/year)
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Figure 4. Phosphorus loading to Florida Bay and the Florida Keys (Gibson et al. 2008; Key for sources in figure: a. 

Gibson et al. 2008, b. Boyer and Keller 2007, c. Rudnick et al. 1999, d. Kruczynski and McMannus 2002, e. 

Leichter et al. 2003).

Table 4 shows a comparison of the 1999 anthropogenic land based nutrient loads (Table 3 totals for 

stormwater and wastewater; FDEP 2008a) converted to metric tons per year to compare with some 

farfield estimates of nutrient loads to the region from Gibson et al. (2008) and Rudnick et al. (1999). 

Land based nutrient sources are a small component of the total nutrient inputs to the Keys. 

NO3-

13000

250

1240 710

5500

500

640

~2000 km

2

8800

TN Inputs and Outputs

(Metric Tons/year)

861 ( e )

“500” ( c )

 3 ( b )

 “38” ( c ) 10 ( b )

 87 ( b )

 90 ( a )

163 ( d )

 “34” ( c )

 “38” ( b )

TP Inputs and Outputs

(Metric Tons/year)
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Table 4. Comparison of total 1999 estimated annual anthropogenic land based (wastewater and stormwater) 

nutrient loadings to the Keys (FDEP 2008a) with some estimated farfield loadings from Florida Bay passes and 

Atlantic upwelling (Gibson et al. 2008) and atmospheric deposition (calculated using atmospheric loading 

estimates in Rudnick et al. 1999) in metric tons year-1. 

- = Empty cell/no data

Source TN

(metric tons year-1) 

TP

(metric tons year-1) 

Keys wastewater and stormwater 438 111.8

Atlantic upwelling 5190 861

Florida Bay (through Middle Keys 

passes)

5500 90

Atmospheric deposition 3040 161.5

 

 

Biological Summary 

The three dominant habitats that make up the coastal marine ecosystems of the Florida Keys are 

seagrass meadows, coral reefs, and mangroves. Seagrasses are the principal component of benthic 

marine habitats in the Keys, occupying over 70% of the FKNMS (Fourqurean et al. 2003). Coral reefs, 

patch reefs, and hardbottom habitats cover approximately 7%, 1%, and 19% of the FKNMS, respectively. 

Mangroves are a dominant feature of the land-sea margin throughout the Florida Keys. 

Seagrasses

The dominant primary producers in the Keys are seagrasses and macroalgae. One of the world’s most 

extensive seagrass beds, approximately 14,000 km2

, surrounds the Florida Keys (Fourqurean and Zieman 

2002). The structure and distribution of seagrass communities varies throughout the Keys. Seagrasses

form extensive meadows and patchy beds, and are also found scattered throughout other habitats

(Fourqurean et al. 2001). The distribution and species composition of seagrasses in south Florida results 

from many factors, with the most important being water depth, water clarity, and nutrient availability 

(Fourqurean et al. 2002). 

Seagrass beds are important habitat for other species, including pink shrimp (Farfantepenaeus), spiny 

lobster (Panulirus argus), queen conch (Strombus gigas), and spotted seatrout (Cynoscion nebulosus) 

(Fourqurean et al. 2001). Lapointe et al. (1994) note that, since the densities of benthic invertebrates 

and fishes that inhabit seagrass meadows are positively correlated with seagrass density and 

productivity, the eutrophication of seagrass meadows could also lead to reductions in secondary 

productivity.

Fourqurean et al. (2001) documented the distribution and abundance of seagrasses in south Florida in a 

larger study area that included the FKNMS from 1995 to 1998 and found T. testudinum to be the most 
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common seagrass at 67.2% of the sites. Other seagrasses observed included Syringodium filiforme at 

38.9% of the sites and Halodule wrightii and Halophila decipens at about 15% at each site. A survey of 

seagrass species composition and density in the FKNMS from 1996 to 1997 found water depth related to 

the density of all observed seagrass species except for Halophila engelmanni. The densities of 

T. testudinum, H. wrightii, and Ruppia maritime were higher in shallow water, while S. filiforme and 

H. decipens density were higher in deeper water (Fourqurean et al. 2002).

There is typically a gradient of water column and sediment nutrient availability, with low N offshore and 

low P nearshore (Boyer and Jones 2002; Szmant and Forrester 1996). In seagrass-dominated systems, it 

can be difficult to determine the actual nutrient status of the water column because of the rapid uptake 

of soluble nutrients (Tomasko and Lapointe 1991). The ratio of N:P in seagrass leaf tissues has been 

used to infer the relative availability of nutrients and spatial patterns in limiting nutrients (Fourqurean 

and Zieman 2002; Burkholder et al. 2007). Fourqurean and Zieman (2002) sampled T. testudinum in the 

Keys and observed strong spatial patterns in the relative amount of N and P in tissues. On the Gulf side 

of the Keys, the N:P ratios indicated P limitation, except at the western margin of Florida Bay. There was 

also a signal of P-limitation in the nearshore area along the Atlantic side of the Keys; however, farther 

offshore the ratios indicated N limitation. It is important to note that factors other than nutrient 

availability, such as variation in light availability or any other factor that limits growth rate, can affect the 

nutrient content of seagrass tissue. The spatial patterns of N:P ratios in this study are consistent with 

estimates of nutrient loading in different areas and sediment nutrient ratios. 

The results of a 14-month fertilization experiment in the FKNMS indicated that there are taxon-specific 

responses to nutrient enrichment and that nutrient limitation differs for nearshore and offshore sites 

and for seagrass and algae (Ferdie and Fourqurean 2004). The authors measured the response of 

seagrasses, macroalgae, epiphytes, and microalgae to additions of N and P fertilizer to assess gradients 

of nutrient limitation nearshore and offshore in the Florida Keys. Sites were located on the east side of 

the upper Keys between the Keys and the reef tract. Fertilization increased both sediment nutrient 

content and plant nutrient content. There was rapid uptake of N by T. testudinum at both nearshore 

and offshore sites, but compared with N, P uptake was delayed. There was an increase in T. testudinum

leaf length, standing crop, and growth rates in response to N, but not P, at offshore sites, implying that 

seagrasses in offshore habitats in the upper Keys are N limited. However, there was no clear increase in 

biomass or primary productivity of seagrasses at nearshore sites in response to added P. Overall, 

nutrient enrichment resulted in increased seagrass biomass at offshore sites and increased macroalgal 

and sediment microalgal biomass at nearshore sites. 

Seagrasses have been monitored in the FKNMS since 1995 (Fourqurean and Escorcia 2009). The FKNMS 

seagrass monitoring program collects data on the distribution and abundance of seagrasses and other 

benthic plants and animals, seagrass tissue nutrient concentration and isotopic composition, and water 

quality (Fourqurean and Escorcia 2009). The general objective of the seagrass monitoring is to measure 

the status and trends of seagrass communities to evaluate progress toward protection and restoration 

of the living marine resources (Fourqurean and Escorcia 2009).
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The FKNMS uses two indicator criteria to assess status and trends in the seagrass communities. The first 

criterion, called the elemental indicator (EI), is based on a conceptual model that predicts that T. 

testudinum is likely to be replaced by faster-growing competitors if nutrient availability is such that leaf 

tissue concentration is near the critical N:P ratio of approximately 30:1. An N:P ratio of 30:1 in seagrass 

leaves hypothetically indicates a balance in the availability of N and P, and monitoring deviations from 

this ratio can be used to infer whether N or P are limiting this species’ growth. This indicator is based on 

the hypothesis that change in the N:P ratio over time, from an N or P limited ratio to a value closer to 

30:1, could indicate eutrophication (Figure 5). 

EI is calculated from the mean absolute difference in N:P from the ideal 30:1 for the 30 permanent 

monitoring sites based on the 10-year (1995–2005) mean N:P ratio at each of those sites. 

Figure 5. Conceptual model of the relationship between seagrass leaf nutrient content and nutrient availability 

in south Florida (Fourqurean and Rutten 2003).

The second indicator criterion, the Species Composition Indicator (SCI), measures whether the 

abundance of the slowest-growing seagrass species, T. testudinum, has changed compared with the 

abundance of other seagrass species. The SCI is based on a dominance-eutrophication gradient 

conceptual model, where each of the six seagrass species can potentially dominate over a range of 

nutrient availability (Figure 6). The conceptual model predicts that species dominance will change as 

nutrient availability changes. However, field evidence suggests that species replacements may take 

place over a decade or more, making it difficult to relate the model prediction to observed response

(Fourqurean and Escorcia 2009). The model predicts that the first responses to eutrophication would be 
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evidenced by an increase in the relative abundance of faster-growing seagrass species (H. wrightii and S. 

filiforme) at the expense of the now-dominant, slow-growing T. testudinum. At later stages of 

eutrophication, macroalgae and microalgae would become the dominant primary producers. 

Figure 6. Conceptual model relating nutrient availability (trophic state) to the abundance of primary producers 

in nearshore marine waters of south Florida (Fourqurean and Rutten 2003).

The change in T. testudinum abundance compared with other species at a site is defined as “SLOW.” 

The distribution and abundance of seagrasses are measured using rapid assessment Braun-Blanquet 

surveys. The SCI is defined as the mean of SLOW over the 30 monitoring sites, where:

ATt = long-term mean abundance of T. testudinum

ASf = long-term mean abundance of S. filiforme

AHw = long-term mean abundance of H. wrightti

Amacroalgae = long-term mean abundance of macroalgal taxa
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The long-term (1995–2005) EI is 8.28 ± 1.47 (± 1 standard error) and the long-term SCI is 0.48 ± 0.04 (± 1 

standard error). Despite a slight decreasing trend in the mean values for both the EI and SCI for 2007 

and 2008, the means were all within the confidence estimate of the long-term averages for 1995 to 

2005 (Figures 7 and 8). Since the EI and SCI are not significantly different from the long-term mean, 

these indices suggest that there have been no significant adverse seagrass responses to nutrients for 

2006-2008 across the FKNMS. 

Figure 7. EI status of seagrasses in the FKNMS for 2006, 2007, and 2008 compared with the long-term mean EI

(dashed line) for 1995 to 2005 (Fourqurean and Escorcia 2009).

Figure 8. SCI status of seagrasses in the FKNMS for 2006, 2007, and 2008 compared with the long-term mean SCI 

(dashed line) for 1995 to 2005 (Fourqurean and Escorcia 2009).

Increased macroalgal abundance, coincident with increased N concentrations, and in some cases, 

increased epiphyte productivity has been observed in nearshore areas of the Keys (Lapointe et al. 1994; 

Collado-Vides et al. 2005; Collado-Vides et al. 2007). Lapointe et al. (1994) observed higher epiphyte 

loads on T. testudinum and H. wrightii at sites closer to shore than at more oligotrophic offshore sites. 

Collado-Vides et al. (2005) sampled seagrass and macroalgal abundance quarterly from 1996 to 2002 at 

28 of the 30 permanent sites in the FKNMS and found the only significant gradient was with distance 

from land, with sites closer to land showing higher values. The principal species of calcareous green 

algae in the seagrass meadows were Halimeda incrassata, H. monile, H. tuna, H. opuntia, Penicillus 
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capitatus, P. dumetosus, P. pyryformis, Rhipocephalus phoenix, Udotea cyathiformis, and U. flabellum. 

Each genus had a unique distribution and seasonal pattern of abundance, with lower abundance in 

winter and higher abundance in summer. In addition, the 4 genera studied increased in abundance at 

most sites over the 7-year study period. Regional-scale gradients in environmental conditions, such as 

salinity and water temperature, did not appear to influence abundance. The higher values of the long 

term trend closer to land could suggest that nutrient influx from land. 

Collado-Vides et al. (2007) used data from the long-term seagrass monitoring program and the water 

quality monitoring program in the FKNMS to detect the long-term abundance trends of macroalgae 

groups and their correlations with median nutrient concentrations for the 30 permanent monitoring 

sites between March 1996 and May 2003. Their analyses suggest that the abundance and long-term 

increases in abundance of major macroalgal groups in the FKNMS were highest in areas with the highest 

availability of N. The dominant group in the seagrass beds was calcareous green algae, dominated by 

Halimeda, followed by the “red other” group, dominated by Laurencia. Results indicated that the 

abundance of almost all macroalgae groups was increasing over the course of the study, suggesting a

“slow and steady” increase of slow-growing calcareous green algae, as opposed to bloom condition. 

Elevated epiphyte loads on seagrass have been observed under eutrophic conditions and in response to 

N and P fertilization (Tomasko and Lapointe 1991; Lapointe et al. 1994; Ferdie and Fourqurean 2004). 

Epiphyte loads on seagrasses in the FKNMS are highly seasonal, with peaks in early spring and minimum 

abundance in early fall (Figure 9; Fourqurean and Escorcia 2009; Fourqurean et al. in press; Lapointe et 

al. 1994). However, Fourqurean et al. (in press) did not find a correlation between epiphyte load on 

turtle grass, T. testudinum, and water column or sediment nutrient concentrations. Fourqurean et al. (in 

press) propose that the top-down grazer removal of epiphytes may obscure the influence of nutrients 

on the epiphyte community.

Figure 9. Seasonality of epiphyte load, averaged across all 30 Level 1 sites, 2001–09 (Fourqurean et al., in press).
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As noted previously, the seagrass beds in the Florida Keys are part of one of the most extensive SAV

beds in the world. Indices used for the seagrass monitoring program in the FKNMS indicate no 

decreased coverage or abundance of seagrass throughout the sanctuary. The various indicators used in 

the FKNMS seagrass monitoring program show no statistically significant change in N:P ratios or 

community composition, when comparing the 2006 to 2008 period with 1995 to 2005 conditions 

(Fourqurean and Escorcia 2009). Although there have been observations of Increased calcareous 

macroalgal growth, it is limited to nearshore areas and is correlated with areas that receive increased N 

loading (e.g. Collado-Vides et al. 2007). Note that calcareous algae are considered a viable benthic 

habitat. Additionally, despite the slow increase in macroalgal abundance at nearshore sites, the 

community composition and coverage of seagrass overall in the FKNMS has not changed since 

monitoring began in 1995 (Collado-Vides et al. 2007; Fourqurean and Escorcia 2009). 

Coral Reefs

The information in the following section is summarized from the State of Coral Reef Ecosystems of the 

Florida Keys report (Donahue et al. 2008), the 2006 Executive Summary of the Coral Reef Evaluation and 

Monitoring Project (CREMP) (Callahan et al. 2007), the 2010 US EPA Water Quality Protection Program 

Steering Committee Presentation (Ruznicka et al. 2010) and the CREMP EPA Steering Committee 

Meeting Presentation Summary (CREMP 2010). 

There have been numerous studies that report loss of coral in recent decades. For example, Chiappone 

and Sullivan (1994) reported changes observed after 4 years of monitoring, from 1989-1992, at two 

hardbottom sites in the Keys. The Craig Key site (CKS) is located about 100 m offshore on the Atlantic 

side of Craig Key. The Fiesta Key site (FKS) is located about 100 m from the shore on the FL Bay side of 

Fiesta Key. At each site, benthic organsims were estimated visually in 1 m2 quadrats and included algae, 

sponges, octocorals, and stony corals. During the study period, there were reductions in species 

numbers and abundance at the FKS. At the CKS, there were increases in abundance of sessile benthic 

invertebrates, with the exception of a loss of coral coverage during 1990-91 due to the mortality of 

Millepora alcicornis (encrusting fire coral) colonies. 

The Florida Fish and Wildlife Research Institute collects annual data on the status of coral habitats in the 

Florida reef tract through the Coral Reef Evaluation and Monitoring Project (CREMP), which began 

monitoring with 40 sites in 1996 and has since expanded to include sites in the Dry Tortugas and along 

the SE coast (Ruznicka et al. 2010, Donahue et al. 2008; Callahan et al. 2007). CREMP sites encompass 

four reef habitat categories: hardbottom, patch reef, and offshore deep and shallow reefs. The 

following summarizes the main long-term trends in benthic cover from 1999-2008 and recent changes 

from 2008 to 2009 (CREMP 2010, Ruznicka et al. 2010).

Overall trends in percent cover from 1999 to 2008 were determined from a generalized mixed model 

regression (Figure 10). Stony coral and sponge were both decreasing (p<0.001), octocoral was 

increasing (p<0.001), and there was no change in macroalgae percent cover (p<0.05) (CREMP 2010). 

Macroalgae cover has been highly variable, but mean cover throughout the project is ~11% (Figure 10). 

However, a significant increase in stony coral was observed between 2008 and 2009, for the first time in 

CREMP’s monitoring history. 
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Figure 10. Line graph of mean annual percent cover for the four major benthic taxa recorded in CREMP image 

analysis (CREMP 2010). Mean percent cover is pooled from 97 stations in the Florida Keys. 

Five of the six most spatially dominant species of stony corals showed a significant decreasing trend in 

percent cover over the period 1996 to 2009 (Figure 11). The only exception is Siderastrea siderea, which 

does not show any significant change. Decreasing trends were observed for Monastraea annularis

(p<0.001), Monastraea cavernosa (p<0.001), Porites astreoides (p<0.001) and Colpophyllia natans

(p<0.001) while there was no change in Siderastrea sidereal (p>0.05). 

The negative trends for the M. annularis complex are most evident in the Lower Keys and Dry Tortugas. 

Overall, 43% (16 of 37) of all CREMP sites showed a negative trend and 69% (11 of 16) of the sites 

showing the negative trend are located in the Lower Keys and Tortugas regions (Figure 12). 

 
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Figure 11. Line graph of the mean annual percent cover for six species of stony corals. Mean percent cover is 

pooled from 97 stations (CREMP 2010). 
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Figure 12. Long term trends of percent cover from 1999-2008 at CREMP sites for a) stony corals and b) 

octocorals (CREMP 2010).

Soft coral, or octocoral, cover has significantly increased during the past 10 years after reaching a low 

point in 1999. Cover of soft corals declined during the initial four years of the project, but has increased 

every year from 1999 through 2004 (Figure 12). Although cover dipped again due to hurricane damage 
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between 2005 and 2007, it was 14.8% in 2009, the highest value ever reported by CREMP. The pattern 

of increased octocoral cover is most evident at the shallow forereef sites and coincides with the loss of 

Acropora palmata and Millepora complanata from these habitats during the mass bleaching and disease 

outbreaks that occurred from 1997-2000 (CREMP 2010).

The incidence of black band disease peaked in 1998, and this disease has not been recorded at more 

than 10 stations since then (Figure 13). White diseases and “other” disease conditions have generally 

declined, although there were peaks in 1998-1999 and 2001-2002. Long spined urchins (Diadema 

antillarum) are herbivores that help keep corals free of algal overgrowth. Observations of D. antillarum

densities have fluctuated, with highs reported in 2002 and 2005 and a general increasing trend since 

1996. There are three species of clionid sponges (Cliona delitrix, C. lampa, and C. caribbaea) monitored 

by CREMP. These taxa are monitored because they can infest and damage coral colonies. By habitat, 

clionid area increased between 2002 and 2006 at hardbottom sites. At shallow, offshore, and patch reef 

sites, the populations have had minor fluctuations in mean clionid area through time. In general, the 

patch reef sites have had higher clionid area than shallow or deep reef sites. 

Figure 13. Number of stations with stony coral disease recorded (Callahan et al. 2007).

In January 2010 Florida experienced one of its coldest 12-day periods on record. Water temperatures 

were depressed below the lethal limit for corals (~16°C) for four to five days. The coldest temperatures 

were observed at exchanges between Florida Bay and The Atlantic. The most significant coral mortality 

was observed at sites closest to shore (Figure 14). Mortality varied by station due to species 

composition. Some stations which were primarily composed by species like M. annularis complex and 

M. cavernosa experienced a greater than 50% reduction in coral cover. In many instances declines in 

octocoral cover exceeded those of stony corals (Figure 14).
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Figure 14. Percent cover comparisons between summer 2009 and February 2010 for a) stony corals and b) 

octocorals at eight stations (CREMP 2010).

Swart et al. (2005) reported temporal and spatial variability in δ13C and δ15N of the tissues and 

zooxanthellae of corals from nearshore and offshore reefs over a 2 year period, from 1995-1996. There 

were no significant seasonal variations in the δ15N of coral or zooxanthellae at any of the sites, but there 

was a significant decrease in δ15N over the course of the study. The decrease was greater in the 

zooxanthellae than the coral tissue and correlated with a decrease in the concentration of NH4

+ and NO2-

in the water column. The δ13C values of the coral tissues did show seasonal patterns at some, but not 

all, sites. The authors note that in the literature there is a discrepancy in interpretation of δ15N values in

marine organisms. In this study, there was no difference in δ15N in coral tissues and zooxanthellae from 

nearshore and offshore environments. Assuming that the δ15N can be considered an indicator of 

anthropogenic influence, these results suggest that the Florida reefs are not affected by anthropogenic 

sources of N. Similar to the N results, they also found no differences in δ13C between the inner and 

outer reefs.

Furman and Heck (2008) tested the single and interactive effects of the urchin (Diadema antillarum)

grazing and effects of experimental nutrient enrichment on macroalgal community dynamics at a site in 

the lower Keys in the summer of 2004. The objective of their study was to assess the relative 

importance of top-down and bottom-up processes in controlling macroalgal recruitment in a subtropical coral reef system. Although algal succession differed from what had been expected, the results 

demonstrated the important role of herbivory in controlling benthic primary production, especially 

related to nutrient enrichment. Results of fish counts and grazing assays suggested that piscine grazing 

was dominant as opposed to the expected echinoderm grazing. Total fish abundance and herbivore 

density was consistently greater at enriched plots, leading to no significant increase in algal biomass at 

the nutrient enriched sites.

Nutrient enrichment is considered to be one of several factors potentially contributing to coral declines. 

Lirman and Fong (2007) evaluated whether proximity to shore and connections to coastal bays (two 

measures of potential land-based sources of disturbance) adversely influenced coral community and 

population structure, and the abundance, distribution, and condition of corals within the Florida Reef 
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Tract. They found that spatial patterns in coral indicators do not appear to be directly related to water 

quality gradients influenced by land-based sources of disturbance. Szmant (2002) evaluated reports 

based on the supporting evidence for nutrient enrichment and other factors that could simultaneously 

affect coral reefs. She proposed that many factors, other than nutrient enrichment, can all be significant 

causes of coral death and also can cause changes in algal cover. These factors include: decreased 

abundance of grazing fishes caused by over fishing, decreases in grazing urchins caused by disease, 

grazing preferences of the remaining grazers, lethal temperature stress, sedimentation, coral diseases, 

and outbreaks of coral predators and sea urchins (possibly as secondary effects of over fishing). In the 

Florida Keys, Szmant (2002) found no reports to indicate that there is a clear connection between 

present water quality conditions and coral health that explain the declines in the reefs. In fact, higher 

algal cover and lower adult coral cover and recruitment has been observed on outer reefs when 

compared with those reefs closer to shore (Chiappone 1996 and Miller et al. 2000 in Szmant 2002). 

Note that the nearshore reefs are directly adjacent to potential sources of land-based nutrients, 

temperature stress, and sedimentation. Since nearshore reefs actually fared better than their offshore 

counterparts, this also suggests that land based sources of pollution, including nutrients, are not directly 

responsible for coral declines.

Additional Biological Resources

There are recreational, commercial, and “headboat” fisheries in the Florida Keys, with fishers including 

both residents and visitors (Donahue et al. 2008). The Keys have been heavily fished, and fishing 

pressure has greatly increased due to augmented fishing power per vessel and a much larger 

recreational fishery (Ault et al. 1997). Estimated fishery exploitation rates suggest that many of the 

Florida Keys reef fish stocks are overfished according to definitions for U.S. fisheries, and results show 

the classic pattern of serial overfishing where more vulnerable species are progressively depleted. Data 

from Ault et al. (1997) also suggest that the biomass composition and abundance of the reef fish 

community may have changed over the past several decades. In 1985, fisheries for conch (Strombas 

gigas) and Goliath and Nassau groupers were closed. In response to overfishing, the FKNMS established 

a series of Sanctuary Preservation Areas (SPAs) in 1997. 

Bohnsack et al. (2004) reported trends in reef fish landings from 1981 to 1992 for the Florida Keys. 

Depending on the year, recreational landings comprised between 40% and 66% of total landings. Reef 

fish accounted for 58% of total fish landings, 69% of recreational landings, and 16% of commercial 

landings. Commercial landings were dominated by invertebrates (spiny lobster, shrimp, and stone 

crabs), which comprised 63% of total landings.

The Florida Fish and Wildlife Conservation Commission (FWC) conducts visual censuses between April 

and October to monitor finfish populations along the Atlantic margin of the Florida Keys in the FKNMS

(Donahue et al. 2008). The goal is to evaluate the relative abundance, size structure, and habitat 

utilization of the reef fish species that comprise local, commercial, and recreational fisheries (Figure 15; 

Table 5).

The FWC began a spiny lobster monitoring program in 1997 to test the effectiveness of no-take zones 

(Donahue et al. 2008). Since protection, mean lobster size in reserves has been larger than legal size, 
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but in exploited areas it has remained below the legal limit most of the time. In most years, the 

abundance of lobsters declined in both reserves and exploited areas during the open season, but the 

declines were lower in the reserves. The decline in abundance inside reserves during the open season 

indicates that the reserves are too small to adequately protect the lobsters from harvest. 

The FWC also monitors the recovery of the queen conch population (Donahue et al. 2008). Since the 

fishery was closed in 1985, there have been signs of recovery. 

Figure 15. Mean fish density by year (2000–06) as recorded during visual surveys in the Florida Keys (Donahue et 

al. 2008).

Table 5. Catch statistics for the 15 more abundant reef fish species observed during the Florida Keys visual 

sampling, 1999–2006. 

Note: Percent (%) is the percentage of the total observations represented by that species; percent occurrence (% Occur) is the percentage of 

samples in which the species was observed; CV is the coefficient of variation. Taxa are ranked in order of decreasing mean density (reference in 

Donahue et al. 2008).
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Water Quality Studies

Inshore-to-offshore trends have been observed in many investigations of water quality in the Keys (e.g. 

Lapointe and Clark 1992; Boyer and Jones 2002; Boyer and Briceño 2009). Lapointe and Clark (1992) 

characterized nutrient concentrations at 30 sites along a gradient from the watershed-coastal zone to 

offshore regions, including sites in Florida Bay and along the reef tract. They observed elevated 

ammonia (NH4

+

), nitrate (NO3

-

), and particulate nitrogen (PN) concentrations in canal and seagrass 

meadows compared with patch and bank reef stations. Soluble reactive phosphorus (SRP) and 

particulate phosphorus (PP) concentrations were significantly higher in canal systems compared with 

seagrass, patch reef, and bank reef stations. Chlorophyll a was also higher in nearshore canal and 

seagrass systems compared with reef stations. 

Boyer and Jones (2002) also reported declining inshore-to-offshore trends for NO3

-

, NH4

+

, TOC, total 

organic nitrogen (TON), and turbidity. The water quality sampling was conducted quarterly at over 200 

stations in the FKNMS and Shelf, and was conducted monthly in Florida Bay, Biscayne Bay, and the 

southwest coast mangrove estuaries. Sampling stations were stratified according to depth, geography, 

distance from shore, proximity to tidal passes, and influence of shelf waters. In the Lower Keys, 

inorganic N and TP were elevated in the Backcountry area. TP concentrations in the Lower Keys 

decreased with distance offshore, but increased along transects in the Upper Keys (Boyer and Jones 

2002). The Upper Keys generally had lower nutrient concentrations than the Lower and Middle Keys. 

Ambient water quality in the Lower Keys and Marquesas is most influenced by the Shelf; the Middle 

Keys is influenced by the Shelf and Florida Bay; the Backcountry is influenced by internal nutrient 

sources; and the Upper Keys water quality is influenced by intrusion of the Florida Current (Boyer and 

Jones 2002). 
Nutrient Criteria Technical Support Document Florida Keys

Draft 28 August 2010

Water quality monitoring in the Florida Keys is collected as part of the larger Southeast Environmental 

Research Center (SERC) water quality monitoring network in south Florida. Stations in the FKNMS are 

sampled quarterly and samples have been collected since it was established in 1995. The information 

below is selected from the 2008 Annual Report of the Water Quality Monitoring Project for the FKNMS 

water quality protection program (Boyer and Briceño 2009). The report includes information on data 

collected between March 1995 and December 2008. Figure 16 shows the study area and subregions, 

and Figure 17 shows the location of the monitoring sites (Boyer and Briceño 2009). The 2008 report 

includes data from 50 quarterly sampling events at 154 stations within the FKNMS. 

Figure 16. Map of study area (Boyer 2010).

Figure 18 shows the distribution of salinity across the region based on median salinities for each station. 

The major freshwater sources to the region are the Shark River/Slough system on the southwest coast of 

the Florida peninsula and the Taylor Slough/C-111 Basin in eastern Florida Bay. Southerly currents along 

the southwest coast and Shelf move water through the Keys passes and may impact the reef tract.

The distribution of dissolved NO3

-

and NH4

+ are very different than that for salinity (Figure 19), with 

highest values in nearshore areas. This implies that factors other than mixing of freshwater affect their 

distributions, such as phytoplankton and seagrass uptake as well as N2 fixation and benthic 

remineralization.

In contrast, TP distributions are very similar to salinity patterns on the west coast (Figures 17 and 20). 

This implies that the source of P on the Shelf is partly terrestrial and partly from the southward 

transport of coastal waters from above Cape Romano. It is important to note that the chlorophyll a

concentrations are tightly coupled to TP availability (Figures 20 and 21).
Nutrient Criteria Technical Support Document Florida Keys

Draft 29 August 2010

Figure 17. Florida International University (FIU) Southeast Environmental Research Center (SERC) Water Quality 

Monitoring Network. Stations in red are sampled as part of the FKNMS monitoring program (Boyer and Briceño 

2009).

Table 6 provides median values for water quality parameters collected as part of the monitoring 

program (Boyer and Briceño 2009). TN values ranged from 0.0546 to 0.692 and 0.044 to 1.358 mg L-1 for 

surface and bottom samples respectively. TP values ranged from 0.003 to 0.0441 and 0.0027 to 0.177 

mg L-1 for surface and bottom samples respectively. Median values were similar for surface and bottom 

values for both TN and TP. Chlorophyll a ranged from 0 to 9.18 μg L-1 with a median of 0.19 μg L-1. 

Surface and bottom DO concentrations were similar with median values of 5.26 and 4.88 respectively.

-83.0 -82.5 -82.0 -81.5 -81.0 -80.5

24.5

25.0

25.5

26.0

26.5

Miami

Gulf of Mexico

Florida Straits

Southeast Environmental Research Center

Florida International University

Funded By SFWMD and EPA

Water Quality Monitoring Network

Quicksands

Dry Tortugas

Marquesas

SW Florida Shelf

Pine Island

Sound

Marco Island

Florida Bay

Biscayne

Bay

Whitewater

Bay

Ten Thousand

Islands

Everglades
Nutrient Criteria Technical Support Document Florida Keys

Draft 30 August 2010

Table 6. Water quality variables measured in the FKNMS, March 1995–December 2008 (Boyer and Briceño 

2009). 

1 mg L-1 = Milligrams per liter

NTU = Nephelometric Turbidity Unit

SU = Standard Unit

μg L-1 = Micrograms per liter

Variable1 Depth Median Minimum Maximum

NO3

-

(mg L-1) Surface 0.00252 0 0.03066

NO3

-

(mg L-1) Bottom 0.00168 0 0.02576

NO2

-

(mg L-1) Surface 0.00056 0 0.00462

NO2

-

(mg L-1) Bottom 0.00042 0 0.00266

NH4

+ (mg L-1

) Surface 0.00686 0.00042 0.10598

NH4

+ (mg L-1

) Bottom 0.0042 0.00014 0.04676

TN (mg L-1) Surface 0.1435 0.0546 0.69188

TN (mg L-1) Bottom 0.1211 0.04438 1.35772

TON (mg L-1) Surface 0.12362 0 0.68754

TON (mg L-1) Bottom 0.1106 0.02688 1.3566

TP (mg L-1) Surface 0.0066 0.003 0.0441

TP (mg L-1) Bottom 0.006 0.0027 0.0177

SRP (mg L-1) Surface 0.0009 -0.0003 0.0234

SRP (mg L-1) Bottom 0.0009 -0.0009 0.0204

Turbidity (NTU) Surface 0.51 0 10.73

Turbidity (NTU) Bottom 0.37 0.01 5.78

Salinity (SU) Surface 36.25 23.49 47.3

Salinity (SU) Bottom 36.37 33.68 38.9

Temperature (°C) Surface 26.96 18.87 33.2

Temperature (°C) Bottom 26.75 18.8 33

DO (mg L-1) Surface 5.26 2.07 9.5

DO (mg L-1) Bottom 4.88 2.97 8 

DO Saturation (%) Surface 80.05 0 134.7

DO Saturation (%) Bottom 73.34 0 119.3

Chlorophyll a (μg L-1) Surface 0.19 0 9.18
Nutrient Criteria Technical Support Document Florida Keys

Draft 31 August 2010

Figure 18. Median salinity, 1995–2009 (Boyer and Briceño 2009).

Figure 19. Dissolved inorganic nitrogen (micromolar[μM]) median, 1995–2007 (Boyer and Briceño 2009).
Nutrient Criteria Technical Support Document Florida Keys

Draft 32 August 2010

Figure 20. TP (μM) median, 1995–2007 (Boyer and Briceño 2009).

Figure 21. Chlorophyll a (μg L-1) median, 1995–2007 (Boyer and Briceño 2009).
Nutrient Criteria Technical Support Document Florida Keys

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The monitoring project resulted in several important findings. First, the study documented elevated 

nitrate in the inshore waters of the Keys (Figure 22). This result was evident from the first sampling 

event in 1995 and continues to be a characteristic of the ecosystem. Interestingly, this gradient was not 

observed in a comparison transect from the Tortugas (no human impact). This type of distribution 

implies an inshore source that is diluted by low-nutrient Atlantic Ocean waters. The presence of a 

similar gradient in TOC and decreased variability in salinity from land to reef also support this concept. 

There were no trends in either TP or chlorophyll a with distance from land. 

Second, the study showed that the highest chlorophyll a concentrations are seen on the Shelf, with a 

strong gradient towards the Marquesas and Tortugas (Figure 21). This is due to the higher TP 

concentrations on the Shelf as a result of the southerly advection of water along the coast.

Figure 22. Dissolved inorganic nitrogen (μM) (Boyer and Briceño 2009).

Waters on the 303(d) List 

The halo zone waters of the Keys were listed as impaired on the 1998 303(d) list, however they have yet 

to be verified as impaired under the Impaired Waters Rule (IWR), pending a decision by EPA on the 

FKRAD. For the purposes of the FKRAD, the halo zone, or bubble WBIDS, waters are defined as 

extending from the coastline out to 500 m. Nearshore waters extend from 500 m to 12,100 m and 

farfield waters, which are assumed to have water quality controlled by outside influences as opposed to 

land based nutrient sources, are beyond the 12,100 m. Figure 23 shows a map of the Keys with the 

WBIDS and regions identified.

In addition to nutrients, waters in the Florida Keys are listed as impaired for several other parameters: 

mercury (in fish tissue), bacteria, and fecal coliform bacteria (Table 7). Mercury impairments are not 

related to anthropogenic nutrient inputs. The relationship between bacteria and anthropogenic 

nutrients is more complex, because although potential sources of bacteria may also be sources of 

nutrients, the presence of fecal coliform or enterococci bacteria does not necessarily indicate the 

presence of anthropogenic nutrients.
Nutrient Criteria Technical Support Document Florida Keys

Draft 34 August 2010

Table 7. Verified impairments in the Florida Keys basin.

Basin 

Group 

Name

Planning 

Unit

Waterbody 

ID (WBID)

Water Segment 

Name

Waterbody 

Type

Waterbody 

Class1

Parameters 

Assessed Using 

the 2001 

Impaired Surface 

Waters Rule 

(IWR)

Concentration 

Causing 

Impairment2

Priority for 

TMDL 

Development3

Comments 

(# Exceedances/# Samples) 

pp = Planning Period vp =

Verified Period4

Florida 

Keys

Upper 

Keys 6005EB

JOHN 

PENNEKAMP 

STATE PARK BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2002, 2003, 2004, 2005, and 

2006.

Florida 

Keys

Lower 

Keys 8073C

SIMONTON 

STREET BEACH 

(KEY WEST) BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2004, 2005, and 2006. 

Florida 

Keys

Lower 

Keys 8073E

SOUTH BEACH 

(KEY WEST) BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2002, 2003, 2004, 2005, and 

2006.

Florida 

Keys

Lower 

Keys 8073F HIGGS BEACH BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2001, 2002, 2003, 2004, 

2005, and 2006.

Florida 

Keys

Lower 

Keys 8073G

REST BEACH 

(KEY WEST) BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2001. (No data available for 

2003, 2004, 2005, and 2006.)

Florida 

Keys

Lower 

Keys 8073H

SMATHERS 

BEACH BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2002, 2003, 2005, and 2006.

Florida 

Keys

Middle 

Keys 8076A

VETERAN'S 

BEACH BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2004 and 2005

Florida 

Keys

Upper 

Keys 8078A

HARRY HARRIS 

COUNTY PARK BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2002, 2004, 2005, and 2006.

Florida 

Keys

Upper 

Keys 8078B

ISLAMORADA 

LIBRARY BEACH BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2004, 2005, and 2006. 

Florida 

Keys

Upper 

Keys 8078C FOUNDER BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2002, 2004, 2005, and 2006.

Florida 

Keys

Lower 

Keys 8080A

BAHIA HONDA 

SANDSPUR BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2005 and 2006

Florida 

Keys

Lower 

Keys 8080B

BAHIA HONDA 

OCEANSIDE BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2001, 2005, and 2006.

Florida 

Keys

Middle 

Keys 8081A

COCO PLUM 

BEACH BEACH 3M Bacteria

Beach 

Advisories > 21 

days/yr High

Beach advisories > 21 days/yr 

in 2001, 2004, 2005, and 2006.

Florida 

Keys

Upper 

Keys 6009 PLANTATION KEY COASTAL 3M Copper > 3.7 μg/L Medium PP = No Data; VP = 21 / 29
Nutrient Criteria Technical Support Document Florida Keys

Draft 35 August 2010

Basin 

Group 

Name

Planning 

Unit

Waterbody 

ID (WBID)

Water Segment 

Name

Waterbody 

Type

Waterbody 

Class1

Parameters 

Assessed Using 

the 2001 

Impaired Surface 

Waters Rule 

(IWR)

Concentration 

Causing 

Impairment2

Priority for 

TMDL 

Development3

Comments 

(# Exceedances/# Samples) 

pp = Planning Period vp = 

Verified Period4

Florida 

Keys

Upper 

Keys 6019

LOWER 

MATECUMBE KEY COASTAL 3M Copper > 3.7 μg/L Medium PP = No Data; VP = 8 / 13

Florida 

Keys

Lower 

Keys 8073

KEY WEST AND 

OUTLYING 

ISLANDS COASTAL 3M Fecal Coliform

> 400 

colonies/100 

ml Low pp = 325/2262; vp = 362/3036

Florida 

Keys

Upper 

Keys 6006A

SOUTH KEY 

LARGO COASTAL 3M Copper > 3.7 μg/L Medium PP = No Data; VP = 42 / 86

Florida 

Keys

Upper 

Keys 6006C

NORTH KEY 

LARGO COASTAL 3M Copper > 3.7 μg/L Medium

PP = No Data; VP = 5 / 8. 

Assessment based on Period 

of Record data

Florida 

Keys

Middle 

Keys 6011A VACA KEY COASTAL 3M Copper > 3.7 μg/L Medium PP = No Data; VP = 19 / 47

Florida 

Keys

Lower 

Keys 6012A BIG PINE KEY COASTAL 3M Copper > 3.7 μg/L Medium PP = No Data; VP = 8 / 21

Florida 

Keys

Lower 

Keys 6013C CUDJOE KEY COASTAL 3M Copper > 3.7 μg/L Medium PP = No Data; VP = 5 / 19

Florida 

Keys

Lower 

Keys 6014A KEY WEST COASTAL 3M Fecal Coliform

> 400 

colonies/100 

ml Low pp = 418/2256; vp = 459/2573

Florida 

Keys

Lower 

Keys 6014A KEY WEST COASTAL 3M Copper > 3.7 μg/L Medium PP = No Data; VP = 9 / 31

Florida 

Keys

Lower 

Keys 6014B STOCK ISLAND COASTAL 3M Copper > 3.7 μg/L Medium PP = No Data; VP = 7 / 14
Nutrient Criteria Technical Support Document Florida Keys

Draft 36 August 2010

 

Figure 23. Map of the Florida Keys with WBIDS and regions (north, central, southcentral, and southern) identified (FDEP 2008a).
Nutrient Criteria Technical Support Document Florida Keys

Draft 37 August 2010

Figure 24. WBID models in the Florida Keys (McClelland 2010).

Numeric Nutrient Criteria Recommendations

FDEP’s evaluation of the biological resources of the Florida Keys indicates that the waters in the 

nearshore zone support a healthy well-balanced community, are attaining the designated use, and have

not shown adverse effects from nutrient enrichment in the nearshore area (state waters beyond 500 m). 

Although there have been changes in some communities (e.g., coral loss) (Table 1), evidence suggests 

that causes other than nutrients are responsible for the responses. Additionally, long term monitoring 

of water quality data indicates consistently low water column nutrient concentrations over time. For 

the halo zone area, however, current nutrient conditions in the canals may not be protective of canals in 

the Keys. While nutrient criteria for the canals and halo zone still need to be determined, FDEP 

supports the nutrient load reductions proposed in the FKRAD in order to improve water quality in the 

halo zone and help ensure that criteria are met in nearshore. 

FDEP is considering two methods for establishing numeric nutrient criteria in the Keys. The first consists 

of adopting the criteria established in the FKRAD, which are based on improving water quality in the 

inshore halo zone to modeled targets (FDEP 2008a). The second approach is to subdivide the nearshore 

waters (state waters beyond 500 m) into zones of similar water quality and establish criteria to maintain 

the current nutrient data distributions, which would continue to support the existing healthy condition. 
Nutrient Criteria Technical Support Document Florida Keys

Draft 38 August 2010

FKRAD recommendations

The FKRAD used two approaches to determine their proposed nutrient targets. One set of targets were

developed based on an insignificant increase in natural background TN and TP levels at 500 m from 

shore. An increase of 10 μg l

-1 TN or 2 μg l-1 TP was considered an insignificant increase at 500 m from 

the shore. Natural background is the predicted model result in the Halo Zone with all of the urban land 

uses changed to natural conditions (Figure 24). The model is described in more detail in the FKRAD 

(FDEP 2008a). According to the model, the targets, which FDEP interprets as long term averages, are 

defined as follows for each area of the Keys (Tables 8-11): 

Table 8. Natural background conditions (modeled) and water quality targets for the northern Keys (FDEP

2008a).

Table 9. Natural background conditions (modeled) and water quality targets for the central Keys (FDEP 2008a).
Nutrient Criteria Technical Support Document Florida Keys

Draft 39 August 2010

Table 10. Natural background conditions (modeled) and water quality targets for the south-central Keys (FDEP

2008a).

Table 11. Natural background conditions (modeled) and water quality targets for the southern Keys (FDEP

2008a).

The second approach outlined in the FKRAD sets the target nutrient concentrations at the 

concentrations measured during the 1985 designation as an OFW. Data from the 1985 designation are 

provided below – the data and ranges represent nutrient thresholds (FDEP 2008a). 
Nutrient Criteria Technical Support Document Florida Keys

Draft 40 August 2010

Table 12. 1985 FDEP OFW water quality data (FDEP 2008a).

For comparison, Table 13 provides the range and means of the modeled targets for both TN and TP. 

Minimum and maximum values are the modeled values for the individual bubble WBIDs and the average 

values are the mean of modeled WBID criteria for either the bayside (N) or Oceanside (S) of the Keys. 

The modeled criteria and the OFW values for bayside TN are comparable, however the modeled 

maximum values for TN for the oceanside WBIDs are lower and result in a lower average value. For TP, 

the range of the modeled values is much less than range of the OFW values and the average of the 

modeled targets are lower for both bayside and oceanside areas. FDEP does not suggest using the OFW 

numbers as targets for water quality criteria because the values are based on a limited number of 

samples taken during a short sampling period. The OFW values are also considerably higher than the 

modeled recommendations outlined in the FKRAD as well as current data on Florida Keys water quality. 

Table 13. Range and means of modeled TN and TP targets for bayside and oceanside bubble WBIDs (FKRAD 

2008).

Modeled water quality targets

TN μg l-1 TP μg l-1

Average Minimum Maximum Average Minimum Maximum

Bayside 353 179 764 10.9 8 13

Oceanside 133 123 142 7.7 7 8 

FDEP Nutrient Criteria Approach

The second approach to setting numeric nutrient criteria is to use water quality data collected by FIU 

SERC as part of the FKNMS water quality monitoring network to establish nutrient criteria that would 

maintain nutrients at the current concentrations that are fully protective of aquatic life. Under this 

approach, TN and TP criteria would be established for sub-basins having similar water quality outside of 

the 500 m limit of the FKRAD criteria. 

Regionalization 

FIU has utilized the data collected as part of their Coastal Water Quality Monitoring Network initiated in 

1992 to spatially aggregate monitoring sites located in south Florida based on similar water quality 

characteristics (Boyer and Briceño 2008). Based on the unique water quality and geologic characteristics 

observed in south Florida, Everglades National Park (ENP) and Florida International University (FIU) have 
Nutrient Criteria Technical Support Document Florida Keys

Draft 41 August 2010

proposed that the estuarine and coastal waters of south Florida be divided into sub-basins for the 

purpose of deriving nutrient criteria. On behalf of ENP, FIU has recently completed an extensive 

statistical characterization of coastal waters from Biscayne Bay to Dry Tortugas to Pine Island Sound. 

The recent analysis was similar to the earlier spatial regionalization method used by FIU, but utilized a 

longer period of record and a modified set of parameters. The analysis used a combination of Principal 

Component Analysis and Hierarchical Clustering of multiple (from 8 to 13) parameters, produced a 

division of the bays as shown in the figure and table below. More detail concerning the analysis 

conducted by Henry Briceño, Joe Boyer, and Peter Harlem from FIU can be found in Appendix A. 

Additionally, the GIS layers with information on the sub-basins as well as FIU’s working files with data 

and statistical analysis are available at a FIU’s ftp site provided earlier. 

This regionalization scheme will be the basis for proposing numeric criteria for each sub-basin. A final 

step in the process will be to evaluate the similarity of the derived criteria with the purpose of 

combining sub-basins with similar criteria (i.e., criteria that are not statistically different) for total 

phosphorus, total nitrogen, and chlorophyll-a.

On the basis of the statistical analysis performed, the south Florida bays and coastal waters, including 

those of the Florida Keys, were divided as detailed in Table 14 and illustrated in Figure 25. 

Table 14. Proposed regionalization for the Florida Keys.

Sub-Basin Map Code Sub-Basin Name

MAR Marquesas

BACK Back Country

BAY Bayside

DRTO Dry Tortugas

OCEAN Oceanside
Nutrient Criteria Technical Support Document Florida Keys

Draft 42 August 2010

Figure 25. Proposed estuarine and coastal nutrient criteria sub-basins for South Florida.
Nutrient Criteria Technical Support Document Florida Keys

Draft 43 August 2010

Proposed Numeric Nutrient Criteria 

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 

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 the Florida Keys 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-
Nutrient Criteria Technical Support Document Florida Keys

Draft 44 August 2010

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 shortterm 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 and will more fully capture climatic cycles (e.g., El Niño, La Niña), 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 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 network of stations in a specified segment of the waterbody; 

and 

• 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 
Nutrient Criteria Technical Support Document Florida Keys

Draft 45 August 2010

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 proposes 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. The proposed long-term targets for the protection 

of a healthy, well-balanced aquatic community in the Florida Keys, as well the annual limits for each 

segment, are provided in Table 15. 
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Draft 46 August 2010

Table 15. Proposed numeric nutrient criteria for all segments of the Florida Keys, including TP, TN, and 

chlorophyll a. For compliance purposes, the long term geometric mean shall not exceed the long term limit nor 

shall the average of all stations in a segment exceed the network average more than twice in a 5 year period. 

The last column shows the value which single station shall not exceed, by segment, more than twice in a 5 year 

period.

Total Phosphorus (μg l-1) 

Segment

Existing Long 

Term 

Geometric 

Mean

Maximum 

Allowed Long 

Term Geometric 

Mean

Annual Geometric 

Mean for a Network of 

Stations (2 of 5 year 

exceedance rate)

Annual Geometric 

Mean for a Single 

Site (2 of 5 year 

exceedance rate)

Marquesas 6.42 7.06 8.12 8.77

Back Country 8.72 9.59 10.88 11.61

Bayside 7.49 8.24 9.75 10.42

Dry Tortugas 5.86 6.45 7.79 8.26

Oceanside 5.66 6.23 7.33 7.89

Total Nitrogen (μg l-1) 

Segment

Existing Long 

Term 

Geometric 

Mean

Maximum 

Allowed Long 

Term Geometric 

Mean

Annual Geometric 

Mean for a Network of 

Stations (2 of 5 year 

exceedance rate)

Annual Geometric 

Mean for a Single 

Site (2 of 5 year 

exceedance rate)

Marquesas 143 157 196 209

Back Country 196 216 247 269

Bayside 196 216 260 279

Dry Tortugas 129 142 184 194

Oceanside 147 162 186 204

Chlorophyll a (μg l-1) 

Segment

Existing Long 

Term 

Geometric 

Mean

Maximum 

Allowed Long 

Term Geometric 

Mean

Annual Geometric 

Mean for a Network of 

Stations (2 of 5 year 

exceedance rate)

Annual Geometric 

Mean for a Single 

Site (2 of 5 year 

exceedance rate)

Marquesas 0.35 0.39 0.50 0.63

Back Country 0.36 0.39 0.50 0.65

Bayside 0.26 0.29 0.37 0.47

Dry Tortugas 0.21 0.23 0.31 0.37

Oceanside 0.19 0.21 0.28 0.33
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Comparison of FKRAD and FDEP approaches

Tables 16 and 17 compare the FKRAD targets for the halo zone with the FDEP proposed criteria for the 

nearshore zone for each of the sub-basins. For both TN and TP, the OFW targets are higher than both 

the modeled targets and the criteria proposed for the sub-basins in the nearshore zone, with the 

exception of the modeled targets for WBIDs 8N and 9N on the bay-side of the upper Keys. In most 

cases, the TP targets in the FKRAD agree with concurrent sub-basin two out of five year annual limits 

calculated by FDEP. There are several TN WBID targets on the bay side of the Keys, however, that have 

considerably higher target concentrations in the FKRAD than those calculated for adjacent sub-basins by 

FDEP in Florida Bay. FDEP is seeking input on the proposed approaches.
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Table 16. Comparison of TN (μg l-1) targets for halo zone modeled WBIDs and OFW targets (from the FKRAD) 

with nearshore FDEP criteria proposed for sub-basins using FIU long-term water quality data. For maps showing 

the locations of WBIDs and sub-basins, see Figures 24 and 25. 

Halo Zone (500 m) targets (FKRAD) Nearshore (500-12,100 m) criteria (FDEP and 

FIU)

Modeled bubble WBIDs OFW Proposed criteria by sub-basin

WBID model ID Target Target Sub-basin name Long term limit (2 

out of 5 year single 

site assessment)

1N 179 Bayside 370 Backcountry 216 (269)

2N 205 Bayside 370 Backcountry 216 (269)

3N 215 Bayside 370 Backcountry 216 (269)

4N 221 Bayside 370 Backcountry 216 (269)

5N 225 Bayside 370 Bayside 216 (279)

6N 248 Bayside 370 Bayside 216 (279)

7N 399 Bayside 370 Bayside 216 (279)

8N 764 Bayside 370 West Florida Bay* 331 (421)

9N 739 Bayside 370 South Florida Bay* 535 (694) 

10N 334 Bayside 370 East Central Florida Bay* 568 (696)

1S 142 Oceanside 288 Ocean 162 (204)

2S 135 Oceanside 288 Ocean 162 (204)

3S 138 Oceanside 288 Ocean 162 (204)

4S 141 Oceanside 288 Ocean 162 (204)

5S 135 Oceanside 288 Ocean 162 (204)

6S 135 Oceanside 288 Ocean 162 (204)

7S 125 Oceanside 288 Ocean 162 (204)

8S 124 Oceanside 288 Ocean 162 (204)

9S 123 Oceanside 288 Ocean 162 (204)

10S 128 Oceanside 288 Ocean 162 (204)

Marquesas 157 (209) 

Dry Tortugas 142 (194)

*Three sub-basins from Florida Bay are included for comparison because they are adjacent to halo zone WBIDs on the bay-side 

of the upper Keys.
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Table 17. Comparison of TP (μg l-1) targets for halo zone modeled WBIDs and OFW targets (from the FKRAD) 

with nearshore criteria proposed for sub-basins using FIU long-term water quality data. For maps showing the 

locations of WBIDs and sub-basins, see Figures 24 and 25. 

Halo Zone (500 m) targets (FKRAD) Nearshore (500-12,100 m) criteria (FDEP and 

FIU)

Modeled bubble WBIDs OFW Proposed criteria by sub-basin

WBID model ID Target Location Target Sub-basin name Long term limit (2 

out of 5 year 

assessment)

1N 11 Bayside 14 Backcountry 9.59 (11.61) 

2N 12 Bayside 14 Backcountry 9.59 (11.61)

3N 12 Bayside 14 Backcountry 9.59 (11.61)

4N 12 Bayside 14 Backcountry 9.59 (11.61)

5N 10 Bayside 14 Bayside 8.24 (10.42) 

6N 10 Bayside 14 Bayside 8.24 (10.42)

7N 13 Bayside 14 Bayside 8.24 (10.42)

8N 11 Bayside 14 West Florida Bay* 13.22 (17.63)

9N 10 Bayside 14 South Florida Bay* 7.65 (9.83)

10N 8 Bayside 14 East Central Florida Bay* 6.48 (7.89)

1S 8 Oceanside 15 Ocean 6.23 (7.89) 

2S 8 Oceanside 15 Ocean 6.23 (7.89)

3S 8 Oceanside 15 Ocean 6.23 (7.89)

4S 7 Oceanside 15 Ocean 6.23 (7.89)

5S 8 Oceanside 15 Ocean 6.23 (7.89)

6S 7 Oceanside 15 Ocean 6.23 (7.89)

7S 7 Oceanside 15 Ocean 6.23 (7.89)

8S 8 Oceanside 15 Ocean 6.23 (7.89)

9S 8 Oceanside 15 Ocean 6.23 (7.89)

10S 8 Oceanside 15 Ocean 6.23 (7.89)

Marquesas 7.06 (8.77) 

Dry Tortugas 6.45 (8.26) 

*Three sub-basins from Florida Bay are included for comparison because they are adjacent to halo zone WBIDs on the bay-side 

of the upper Keys.
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Appendix A. Permitted facilities and landfills in the Florida Keys basin by planning unit (FDEP 2008b).
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