Site-Specific Information 

in Support of Establishing 

Numeric Nutrient Criteria in 

Biscayne Bay

Florida Department of Environmental Protection

Tallahassee, FL 32399

August 18, 2010 
Nutrient Criteria Technical Support Document Biscayne Bay

Draft ii August 2010

Table of Contents

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

Geographic and Physical Description ..................................................................................... 3

Sources and Fates of Nutrients .............................................................................................. 5

Biological Summary............................................................................................................... 8

Seagrasses..................................................................................................................................9

Coastal Wetlands......................................................................................................................14

Coral Reefs...............................................................................................................................14

Other Biological Resources........................................................................................................14

Summary of Existing Water Quality Studies ......................................................................... 15

Waters on the 303(d) List..................................................................................................... 16

Proposed Numeric Nutrient Targets..................................................................................... 28

Regionalization.........................................................................................................................28

Proposed Numeric Criteria ........................................................................................................30

Magnitude ...............................................................................................................................30

Frequency and Duration............................................................................................................30

Summary of the Proposed Criteria.............................................................................................31

References .......................................................................................................................... 34

Appendix A. Impaired Waters in the Biscayne Bay Basin ..................................................... 38

Appendix B: Overview of FDEP Approaches for Nutrient Criteria Development in 

Marine Waters......................................................................................................... 42
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List of Tables

Table 1. Checklist of nutrient enrichment symptoms in Biscayne Bay ......................................................... 2

Table 2. Major nutrient sources by region in Biscayne Bay (Caccia and Boyer 2005). ................................ 5

Table 3. Ten-year (1994–04) annual mean, wet season, and dry season canal inputs in cubic feet 

per second (cfs) from the canals in the three zones of Biscayne Bay (Caccia and Boyer 

2005). ............................................................................................................................................ 7

Table 4. Mean canal loads of NOx

-

, NH4

+

, DIN, TP (all in tons per year), and DIN:TP (molar) to the 

bay regions and the entire bay, 1994–2002 (data from Caccia and Boyer 2007)......................... 8

Table 5. Comparison of DIN loads to regions of Biscayne Bay (tons per year) from the 

atmosphere, canals, and ground water (data from Caccia and Boyer 2007). .............................. 8

Table 6. Comparison of TP loads to regions of Biscayne Bay (tons per year) from the atmosphere, 

canals, and ground water (data from Caccia and Boyer 2007)..................................................... 8

Table 7. Summary statistics for water quality in Biscayne Bay, 1994–2003, by season (all 

concentrations are mg l-1, except chlorophyll a, which is μg l-1) (Caccia and Boyer 2005)..........15

Table 8. Waterbodies on the 2010 Verified List for impairments in Biscayne Bay (FDEP).........................23

Table 9. Estuarine waterbodies in Biscayne Bay that are proposed for delisting (FDEP). .........................27

Table 10. Proposed regionalization for Biscayne Bay. ...............................................................................28

Table 11. Proposed numeric nutrient criteria for all segments of the Biscayne Bay, 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. .........................................................................................................................................32
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List of Figures

Figure 1. Map of the southeast Florida coast, showing Biscayne Bay, its protected areas, and 

BNP boundaries............................................................................................................................. 4

Figure 2. Land uses and sources of nutrient inputs to Biscayne Bay (Caccia and Boyer 2005).................... 6

Figure 3. Map of Biscayne Bay habitats (modified from J. Serafy). ............................................................. 9

Figure 4. Location of SAV monitoring sites (CERP 2010)............................................................................11

Figure 5. Location of fixed benthic and random stations (CERP 2010). .....................................................12

Figure 6. Probability of occurrence of seagrasses in relation to mean salinity during the wet 

season fitted with logistic regression (CERP 2010). ....................................................................13

Figure 7. Percent cover of SAV in nearshore habitats of Biscayne Bay, 2003–08 (CERP 2010). ................14

Figure 8. Zones of similar water quality in Biscayne Bay (Boyer and Briceño 2008). ................................17

Figure 9. Box-and-whisker plots of water quality in the Alongshore zone (Boyer and Briceño 

2008). ..........................................................................................................................................18

Figure 10. Box-and-whisker plots of water quality in the Inshore zone (Boyer and Briceño 2008). ..........19

Figure 11. Box-and-whisker plots of water quality in the Main Bay zone (Boyer and Briceño 

2008). ..........................................................................................................................................20

Figure 12. Box-and-whisker plots of water quality in the South Card zone (Boyer and Briceño 

2008). ..........................................................................................................................................21

Figure 13. Box-and-whisker plots of water quality in the North Bay zone (Boyer and Briceño 

2008). ..........................................................................................................................................22

Figure 14. Proposed estuarine and coastal nutrient criteria sub-basins for south Florida. .......................29
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Executive Summary

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

with local scientists, to support the development of numeric nutrient criteria for Biscayne Bay. 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. 

All waters in Biscayne Bay are designated as Class III, with a designated use of fish consumption and

recreation, propagation and maintenance of a healthy, well-balanced population of fish and wildlife. 

Biscayne Bay is also a designated Outstanding Florida Water (OFW). 

Watershed development has led to a variety of intermittently observed adverse effects in portions of 

Biscayne Bay, including hypersalinity, algal blooms, seagrass mortality, and the loss of some fish species 

(Table 1; South Florida Water Management District [SFWMD] 1995). Water quality appears to be 

related to land use in the basin, and water quality in the bay differs among the North, Central and South 

regions. 

Additionally, nutrients exhibit a declining gradient from the land to the open bay (Caccia and Boyer 

2005). Sources of nutrients include agricultural activities, landfill leachate, stormwater runoff (both 

urban and residential), atmospheric deposition, and sewage contamination (Caccia and Boyer 2005). 

Despite the proximity of Biscayne Bay to these human activities, chlorophyll a concentrations in the bay 

remain very low, with the highest levels observed (in North Bay) still usually less than 3 micrograms per 

liter (μg l-1). 

Table 1 shows a checklist of nutrient enrichment symptoms and describes whether they have occurred, 

either historically or currently, in Biscayne Bay. Despite rapid urbanization and hydrologic changes to 

the south Florida system, the 1999 National Estuarine Eutrophication Assessment report found that

Biscayne Bay was predominately an oligotrophic system (National Oceanic and Atmospheric 

Administration [NOAA] 1999). 

The proposed numeric nutrient criteria are based on a “maintain existing conditions” approach using the 

water quality monitoring data collected from 1995 to 2009 by Florida International University’s (FIU) 

Southeast Environmental Research Center (SERC). FDEP recommends regionalizing the bay into subbasins with similar water quality characteristics, and believes that Biscayne Bay is supporting healthy 

biological communities and meeting its designated use during this period of record. For each sub-basin, 

the proposed criteria are expressed as a long-term geometric mean nutrient concentration target 

derived as the long-term geometric mean concentration plus 10%. 
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Table 1. Checklist of nutrient enrichment symptoms in Biscayne Bay

- = Empty cell/no data

Response Variable Observed 

Historically 

or 

Currently?

Explanation Source

Low dissolved 

oxygen (DO) 

(hypoxia/anoxia)

Yes Low DO is localized in the North Bay near canal 

inputs, where it is chronically low due to 

stratification. 

Caccia and Boyer 2005, 

2007

Reduced clarity Yes Turbidity is an issue in parts of North Biscayne Bay

near historical dredge-and-fill activities and near 

industrial complexes, such as the Port of Miami.

Caccia and Boyer 2005 and 

references within; Harlem 

1979

Increased 

chlorophyll a

concentrations

Yes Median chlorophyll a concentrations have 

increased in the North Bay, but chlorophyll a

concentrations are still generally below 3 μg l-1. 

Boyer and Briceño 2008

Phytoplankton 

blooms (nuisance 

or toxic)

Yes Historically (1925–76), the Miami River discharged 

nutrients into northern Biscayne Bay, leading to 

occasional blooms. In 2005–06, there was a 

diatom bloom in Blackwater Sound.

Markley 2010; 

Harlem 1979

Problematic 

epiphyte growth 

No None reported. - 

Problematic 

macroalgal growth

No Drift algae is sometimes found near canal 

discharge sites but does not adversely affect the 

bay proper. 

Biber and Irlandi 2006

Submerged 

aquatic vegetation 

(SAV) community 

changes or loss

Yes Although SAV is stable in most of Biscayne Bay, 

the abundance and community composition of 

seagrasses have changed near canal outputs, 

potentially due to freshwater inputs. SAV remains

healthy throughout the interior of the bay.

Comprehensive Everglades 

Restoration Plan (CERP)

2010; Meeder and Boyer 

2001

Emergent or 

shoreline 

vegetation 

community 

changes or loss 

Yes Diversion of fresh water and development of 

shorelines have reduced mangrove habitat.

Browder et al. 2005

Coral/hardbottom

community 

changes or loss 

Yes Coverage and species abundance have declined, 

but there is no indication that nutrients were 

responsible.

Robles et al. 2005

Impacts to benthic 

community

No None reported. - 

Fish kills Yes Fish kills of generally limited extent and severity

have occurred from low DO, cold, red tide, fishing 

violations, and other unknown causes.

Florida Fish and Wildlife 

Conservation Commission 

(FWCC) Fish and Wildlife 

Research Institute (FWRI) 

2010
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Geographic and Physical Description

Biscayne Bay is located along the coast of Miami-Dade and northern Monroe Counties. The bay is 

bordered to the west by the mainland of Florida and to the east by a series of barrier islands and the 

northern Florida Keys (Comprehensive Everglades Restoration Plan [CERP] 2010). It is a shallow 

carbonate estuary with an area of approximately 700 square kilometers (km2

) and a watershed area of 

about 2,429 km2

 (Figure 1; Caccia and Boyer 2005). 

In general, the bay is shallow and well mixed. Depth ranges from about 0.5 to 3.0 meters (m), except for

dredged areas, where depths may exceed 12 m (Caccia and Boyer 2007; Roessler et al. 1975 in Caccia 

and Boyer 2005). The width of the bay ranges from 1.6 to 16 km, and its length is approximately 88.5 

km, extending in a southwesterly direction from Dumfoundling Bay in the north to Barnes Sound in the 

south (Caccia and Boyer 2007). Tidal exchange with the Atlantic Ocean occurs through the Safety Valve, 

a wide series of shoals and shallow cuts in central Biscayne Bay, and through narrow cuts and creeks in 

other parts of the bay (CERP 2010).

Biscayne Bay was designated as an OFW in 1978 and is a state Aquatic Preserve. The bay also includes 

Biscayne National Park (BNP), which is surrounded by natural areas under some form of protection, 

including marine waters and lands managed by the state (John Pennekamp Coral Reef State Park, Bill 

Baggs Cape Florida State Park, and Biscayne Bay Aquatic Reserve) or the federal government (Florida 

Keys National Marine Sanctuary). 

The bay was historically divided into three general areas: North, Central, and South Bays. North 

Biscayne Bay is the most altered by dredging and bulkheading, and approximately 40% of the area is too 

deep or turbid to support productive bottom habitats. Central Biscayne Bay, which includes much of 

BNP, is more marine and heavily influenced by tidal flushing. South Biscayne Bay includes Card Sound, 

Little Card Sound, Barnes Sound, and Manatee Bay. This area has seen the largest reduction in historical 

freshwater flows and becomes hypersaline during periods of low rainfall. 

Biscayne Bay is further subdivided into the following regions by water chemistry characteristics: north 

central inner (NCI), north central outer (NCO), south central inner (SCI), south central middle (SCM), 

south Card Sound (SCS), south Manatee Bay (SMB), and south Barnes Sound (SBS).

The Biscayne Bay Basin currently has intensive urban development in the northern portions and 

extensive agricultural development in the southern regions (Irlandi et al. 2004). Biscayne Bay, Florida 

Bay, and the Everglades were once part of a larger system of hydrologically interconnected wetlands 

and coastal lagoons, with Biscayne Bay receiving and draining a significant amount of fresh water from 

the Everglades to the Atlantic (Robles et al. 2005). To promote agricultural and urban uses, a series of 

massive water diversion and drainage projects in south Florida (Light and Dineen 1994) transformed the 

natural hydrology of the region, from a process driven by diffuse sheet flow to one now driven by pulsed 

releases of water. Within the bay, the system has been further altered as a result of the construction of 

bridges, artificial islands, and an Intracoastal Highway, and the dredging of the bay bottom (Robles et al.

2005).

The 2009 draft RECOVER SSR (CERP 2010) notes the importance of the constructed canals on the 

hydrology of Biscayne Bay. There are 12 major conveyance canals that discharge fresh water into the 

bay. Flood control canals drain the watershed, and the timing and quality of freshwater discharges have 

been significantly modified from historical natural conditions. A number of adverse effects—such as 

lowered regional and coastal water tables (Parker et al. 1955), reduced water storage in the watershed, 
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decreased ground water flow, and the elimination of natural tributaries—have occurred as a result of 

the construction of major canals and dredging of natural tributaries (CERP 2010). In addition, 

constructed drainage systems have resulted in pulsed, point source discharges that degraded estuarine 

habitat near canal mouths by creating biologically damaging zones of bottom scouring and rapid salinity 

fluctuation (CERP 2010). Draining the watershed and opening inlets have greatly affected natural 

salinity gradients and reduced or eliminated critical estuarine habitat for bay species requiring low- to

moderate-salinity waters (CERP 2010).

Figure 1. Map of the southeast Florida coast, showing Biscayne Bay, its protected areas, and BNP

boundaries. 
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Sources and Fates of Nutrients

Historically, coastal wetlands and sloughs connected the Everglades to Biscayne Bay. Point and 

nonpoint sources of nutrients now reach the bay, either directly as discharge from canals, which drain 

much of the watershed, or indirectly as ground water. Flood control canals have hydrologically isolated 

tidal creeks and changed the timing and delivery of fresh water to the coastal system from what was 

slow seepage to larger pulsed inputs. The timing of freshwater delivery is also altered for agricultural 

purposes and in anticipation of storm events.

Activities associated with CERP will change terrestrial flows within the upstream watershed, potentially 

increasing freshwater and nutrient inputs to Biscayne Bay. CERP aims to restore some of the historical 

flow and the natural timing and distribution of water to enhance the Everglades’ wetlands and 

associated lakes, rivers, and bays in south Florida (CERP 2010). Historical volumes of water to Biscayne 

Bay were undoubtedly higher than present, but the degree to which external nitrogen (N) and 

phosphorus (P) inputs affected the system is unknown because no predevelopment water quality data 

exist (CERP 2010). The 2009 Draft RECOVER SSR noted the importance of freshwater inputs to the 

system and the need to balance the positive effects of freshwater inputs with the negative impacts of 

their concomitant nutrient loads (CERP 2010): “... it follows that a balance exists whereby the benefits 

afforded by increased flow and improved salinity regime for faunal utilization are not undone by 

potential adverse effects from increased nutrient loading.” 

The water quality of Biscayne Bay is highly dependent on land use and influence from the surrounding 

watershed (Caccia and Boyer 2005). Water quality at stations sampled nearer to the coast, with greater 

canal inputs, are more affected by nutrient loading sources than stations farther from shore (Caccia and 

Boyer 2005). Nutrient sources to Biscayne Bay include urban stormwater runoff, sewage contamination, 

landfill leachate, sewage plant discharge, agricultural runoff, groundwater inputs, and atmospheric 

deposition. Figure 2 shows land uses in the basin and the locations of major sources of nutrient inputs; 

these sources differ by region. Table 2 summarizes the major sources of nutrients to each of the regions 

of Biscayne Bay. 

Table 2. Major nutrient sources by region in Biscayne Bay (Caccia and Boyer 2005). 

Region Nutrient Sources

North Bay • Urban stormwater

• Sewage contamination

• Shoreline erosion from the action of waves against unstabilized shorelines

• Dredging

• Munisport landfill

Central Bay • Residential stormwater

South Bay • Runoff from the south Dade County agricultural basins

• Black Point landfill leaching

• Black Point Sewage Treatment Plant discharge

• Homestead Air Force Base

 
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Figure 2. Land uses and sources of nutrient inputs to Biscayne Bay (Caccia and Boyer 2005).
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Most nutrients derived from watershed sources are delivered to Biscayne Bay via the canal system. 

North Bay receives the most freshwater canal input, followed by South Bay and Central Bay, which 

receive minimal canal inputs (Table 3). The Miami River, Snake Creek, and Little River deliver 

approximately half of the entire freshwater contribution to Biscayne Bay in the North Bay region (Caccia 

and Boyer 2005, 2007). Table 3 shows the annual mean, wet season, and dry season discharge from the 

canals in each region of the bay. 

Table 3. Ten-year (1994–04) annual mean, wet season, and dry season canal inputs in cubic feet per 

second (cfs) from the canals in the three zones of Biscayne Bay (Caccia and Boyer 2005).

Caccia and Boyer (2007) calculated nutrient loads from canals, ground water, and the atmosphere to 

Biscayne Bay. For the canals, they observed that nitrogen oxide (NOx

-

) loading was triple that of 

ammonia (NH4

+

) and was the most abundant form of dissolved inorganic nitrogen (DIN) (Table 4; Caccia 

and Boyer 2007). NOx

- loading from Mowry and Princeton canals into South Bay accounted for 74% of 

total NOx

- to the bay (Table 5), reflecting the contribution of more agricultural land use in that region. 

North Bay, however, received the largest NH4

+ load from the Miami River, Little River, and Snake Creek, 

which together accounted for 74% of the total NH4

+ load. Overall, DIN and freshwater flow were 

correlated. 

Like NH4

+

, the highest total phosphorus (TP) loads were also from the Miami River, Little River, and 

Snake Creek to North Bay. These 3 inputs accounted for 60% of the entire canal TP load to the bay. 

However, unlike DIN, TP load was not significantly related to flow. 
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Caccia and Boyer (2007) also compared DIN and TP loads from canals to Biscayne Bay with loads from 

atmospheric wet deposition and ground water (Tables 5 and 6, respectively). In the North and South

regions of Biscayne Bay, the DIN contributions from canals were significantly higher than from the 

atmosphere. For TP, however, contributions from canals were higher than the atmosphere only in 

North Bay. Although ground water loading estimates are only given for South Bay, they show that the 

relative load contribution is comparable to atmospheric or canal inputs for DIN and TP, respectively. 

Table 4. Mean canal loads of NOx

-

, NH4

+

, DIN, TP (all in tons per year), and DIN:TP (molar) to the bay 

regions and the entire bay, 1994–2002 (data from Caccia and Boyer 2007).

Region NOx

- NH4+ DIN TP DIN:TP

North Bay 235 312 547 18.6 65.1

Central Bay 39 28 67 3.4 43.6

South Bay 1,021 52 1,073 5.4 440.0

Biscayne Bay 1,294.5 392.6 1,687.2 27.5 143.5

Table 5. Comparison of DIN loads to regions of Biscayne Bay (tons per year) from the atmosphere, 

canals, and ground water (data from Caccia and Boyer 2007). 

- = Empty cell/no data

North Central South

Atmosphere 46 51 134

Canal 547 67 1,073

Ground water - - 141

Table 6. Comparison of TP loads to regions of Biscayne Bay (tons per year) from the atmosphere, 

canals, and ground water (data from Caccia and Boyer 2007). 

- = Empty cell/no data

North Central South

Atmosphere 2.8 3.1 8.1

Canal 18.6 3.4 5.9

Ground water - - 5.4

Biological Summary

The principal habitat types in Biscayne Bay are seagrass meadows, coastal wetlands (including 

mangroves), and the coral reef community (Robles et al. 2005). Figure 3 shows the distribution of 

habitat types in Biscayne Bay. The bay’s habitats support a variety of wildlife, including fish, 

invertebrates, dolphins, manatees, sea turtles, American crocodiles, bald eagles, and many species of 

wading birds (Caccia and Boyer 2005).

Prior to the development of Miami-Dade County, mangroves and herbaceous wetlands bordered much 

of Biscayne Bay (CERP 2010). Productivity is largely benthic based because of the bay’s shallow depths 

and naturally clear waters (Roessler and Beardsley 1974). There is heavy development along North Bay, 

although benthic communities do exist and are dominated by seagrasses intermixed with calcareous 
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green algae (CERP 2010). There is less development along Central and South Bay, and natural mangrove 

wetlands are intact along the western shore and eastern barrier islands (CERP 2010). The benthic 

communities in Central and South Bay comprise several seagrass species, including Thalassia testudinum

(turtle grass), Halodule wrightii (shoal grass), Syringodium filiforme (manatee grass), and algae. There 

are also hardbottom communities of hard and soft corals, sponges, and other organisms found in 

distinct patches along the north-south axis of the middle of the bay (CERP 2010).

 

Figure 3. Map of Biscayne Bay habitats (modified from J. Serafy).

Seagrasses

The predominant seagrass in Biscayne Bay is T. testudinum (Irlandi et al. 2002). Other seagrasses 

include S. filiforme and H. wrightii. Combined, these seagrasses cover approximately 65% of the bay 

(Miami-Dade Department of Environmental Resources Management [DERM] 1985). The seagrass cover 

is most extensive in Central Bay, covering 75% of the bottom, and least extensive in North Bay, covering 

only 25% of the bottom. The lower percentage coverage in the Northern Bay is predominately due to 

the influence of dredge-and-fill activities and canal discharge. The bottom of South Bay is over 50% 

seagrass and approximately 35% hardbottom. Seagrass species generally shift from H. wrightii in 
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nearshore waters to T. testudinum interspersed with H. wrightii and S. filiforme in deeper waters 

(Lirman and Cropper 2003). 

As part of CERP restoration activities, there will likely be a diversion of fresh water from canals that flow 

into Biscayne Bay west to the Everglades. Much of the research described below focuses on the role of 

freshwater influxes on the structure and function of the seagrass community. 

Biber and Irlandi (2006) characterized the species composition, biomass, and percent cover of drift algae 

and rhizophytes at T. testudinum-dominated sites with different salinity conditions from 1996 to 1999. 

Sites were canal influenced (low salinity), had natural sheet flow conditions (intermediate salinity), or 

had oceanic conditions (normal 35 practical salinity units [psu] salinity). The authors suggest that canal 

discharge poses an unnatural stress to the seagrass habitats of western Biscayne Bay. While stress 

effects were not particularly obvious in the standing stock biomass of T. testudinum, the influence of the 

canal discharge was evident in the composition of the macroalgal community found within seagrass 

beds at the three salinity regimes—in particular, changes in abundance and dominance from drift algae 

at the canal sites to rhizophytic algae at the oceanic sites. 

It is important to note that macroalgae are an important component of the benthic community of 

Biscayne Bay. The many species of algae in the bay are roughly grouped into drift algae (e.g., Chondria

spp., Laurencia spp.) and rhizophytic algae (e.g. Caulerpa spp., Halimeda spp., and Penicillus spp.) (Biber 

and Irlandi 2006). Clumps of detached drift algae may alter seagrass productivity through shading; 

however, benthic rhizophytic algae can facilitate seagrass succession by stabilizing sediments and adding 

organic matter. Irlandi et al. (2004) investigated drift algae-epiphyte-seagrass interactions in a T. 

testudinum meadow and found no negative response on the short-term growth of T. testudinum by drift 

algae.

Meeder and Boyer (2001) found that high NH4

+ concentrations associated with the Black Point landfill in 

South Bay were correlated with the decreased abundance of T. testudinum and increased abundance of 

filamentous red algae cover. Szmant (1987) found nutrient-related canal impacts at the discharge points 

of the Mowry and Princeton Canals. These included increased periphyton growth on artificial seagrass 

blades and the replacement of T. testudinum with H. wrightii. 

Irlandi et al. (2002) determined the biomass, morphometrics, and production of T. testudinum at sites 

exposed to varying degrees of freshwater runoff to evaluate the possible effects of changes in 

freshwater inputs to Biscayne Bay. Their results indicate that freshwater runoff only affected the 

biomass and morphometry of T. testudinum during years with particularly high rainfall, where the 

seagrasses were exposed to prolonged conditions of low salinity. They concluded that as long as 

reductions in freshwater inputs to Biscayne Bay do not result in hypersaline conditions, the diversion of 

fresh water to the Everglades should have a positive effect on T. testudinum. 

In addition to the research described above, there are several ongoing long-term monitoring programs 

collecting data on SAV and water quality in Biscayne Bay, specifically to establish baseline conditions 

against which changes associated with the implementation of CERP can be assessed (CERP 2010). 

Figure 4 shows the locations of monitoring sites in the south Florida estuaries. For Biscayne Bay, 

monitoring programs include nearshore and benthic monitoring of SAV (CERP 2010 and references 

within).
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Figure 4. Location of SAV monitoring sites (CERP 2010). 

Miami-Dade DERM, in partnership with SFWMD, has conducted a benthic habitat monitoring program in 

Biscayne Bay since 1985. The monitoring program was initiated with 13 fixed locations throughout the 
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bay, 10 of which remain active. Figure 5 shows the study area. Sampling was conducted quarterly at 

fixed strategic locations from 1985 to 1996, when it was decreased to once annually. In addition, 

stratified random sampling has been conducted annually since 1999 (Fourqurean et al. 2002).

Figure 5. Location of fixed benthic and random stations (CERP 2010).

The nearshore (less than 500 m from shore) benthic habitats of Biscayne Bay have been monitored since 

2003 to evaluate the spatial patterns of SAV abundance in relation to distance from shore and the inflow 

of fresh water from canals, ground water, and overland sources (Lirman et al. 2008; CERP 2010). The 

monitoring project provides baseline data for seasonal species composition and distribution and SAV 

abundance in the nearshore habitat, which is sensitive to changes in freshwater input.

The main results from the DERM and Lirman et al. (2008) monitoring programs are as follows: 

• Patterns of T. testudinum cover in South Bay follow relationships with salinity 

regimes, water depth, and sediment depth. All three seagrass species showed 

significant relationships with mean salinity; H. wrightii had a higher probability of 

occurrence at low mean salinity, while T. testudinum and S. filiforme had a higher 

probability of occurrence at high mean salinity (Figure 6).
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• The abundance of T. testudinum increased linearly with increasing distance from 

shore and depth, while the abundance of H. wrightii had the opposite pattern.

• H. wrightii and S. filiforme have had stable benthic cover since 2002, while T. 

testudinum showed a steady decline from greater than 40% in 2003 to less than 20% 

in 2008, and macroalgal cover remained stable between 2003 and 2008 (Figure 7).

• The proportion of the densest patches, which had greater than 70% cover, declined 

greatly from 2003 to 2008, suggesting that the decline in cover was especially 

pronounced within the densest T. testudinum beds.

• H. wrightii is second to T. testudinum in overall presence. Reviews of 3-year 

groupings of data show H. wrightii was consistently found in the northern and 

southern regions, with low (less than 5%) to moderate cover (25%). It also occurs 

sporadically along the western shore, and in the hardbottom areas at low cover (less 

than 5%). S. filiforme is primarily located in the northern and southern sections, with 

infrequent records in western nearshore and eastern polygons.

• Low percent cover (less than 5%) is common in the hardbottom habitats of the 

southern mid-bay. Additional areas of lower cover also occur in habitats with 

greater depth (northern and southern) and/or lower salinity. 

Figure 6. Probability of occurrence of seagrasses in relation to mean salinity during the wet 

season fitted with logistic regression (CERP 2010).
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Figure 7. Percent cover of SAV in nearshore habitats of Biscayne Bay, 2003–08 (CERP 2010).

Coastal Wetlands

Biscayne Bay has a narrow strip of coastal wetlands consisting primarily of mangroves and sawgrass. 

Development has reduced the extent and composition of the wetlands by reducing freshwater inputs 

(via diversion for agriculture or residential uses) (CERP 2010). According to the 2009 Draft RECOVER SSR

(CERP 2010), the coastal wetlands are an important influence on the inshore areas of the bay and 

numerous important sport and commercial fish that have been monitored in the mangrove shoreline 

zone since 1998 as a gauge of Everglades restoration impacts (CERP 2010). Although little is known 

about predevelopment communities, community composition is likely to change further as restoration 

efforts increase natural freshwater flows to the area.

Coral Reefs 

The reef tract of BNP is a complex assortment of approximately 4,000 patch reefs located on a shallow 

Holocene platform on the eastern edge of Hawk Channel (Jaap 1984 in Robles 2005). Coral reefs in 

Florida face a number of different stressors. The Florida Reef Tract and adjoining Biscayne Bay are sites 

of extensive recreational and commercial fishing, an activity that has a large impact on coral reefs 

(Robles 2005). Additional stressors include coral bleaching, diseases, water pollution, physical impacts 

(such as groundings, dredging activities, and beach renourishment), tropical storms, and winter cold 

fronts (Banks et al. 2005). The areal coverage and species abundance on coral reefs within BNP and the 

south Florida Reef Tract have declined over the past several decades, although the cause of the decline 

is not understood (Dustin and Halas 1987; Porter and Meier 1992). 

Other Biological Resources

The seagrass habitat supports many other organisms, including pink shrimp (Penaeus duorarum), spiny 

lobster (Panulirus argus), and many recreationally and commercially important fish such as spotted sea 

trout (Cynoscion nebulosus), red drum (Sciaenops ocellata), snook (Centropomus undecimalis), and 
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mangrove snapper (Lutjanus griseus) (Robles et al. 2005). Biscayne Bay is also a refuge for juvenile spiny 

lobster, and a large portion of the bay is a designated lobster sanctuary (Robles et al. 2005). 

Summary of Existing Water Quality Studies

Water quality in Biscayne Bay is generally good, with diminished quality limited to the North Bay and the 

western margin of the bay. Water quality has been monitored in Biscayne Bay for over 30 years through 

state, local, federal, and university partnerships. Sources of water quality data include FIU, University of 

Miami (UM), NOAA, BNP, and DERM. 

Nutrient loads and concentrations in Biscayne Bay are strongly driven by canal inputs (Caccia and Boyer

2007; Browder et al. 2005). Concentrations of several water quality parameters in a number of the 

canals and rivers that discharge to the bay are high compared with the open waters of the bay (Browder 

et al. 2005). Precipitation patterns have a great impact on the bay, both directly as rainfall and 

indirectly by influencing runoff and canal discharge. 

Caccia and Boyer (2005) report water quality results for sampling conducted from 1994 to 2003 by 

season (Table 7). TP values ranged from 0.00 to 0.049 milligrams per liter (mg l-1) with a median of 0.006 

mg l-1. All N species concentrations were highest in the wet season, when canal inputs are greater. 

There was also a strong gradient from inshore out to the open bay. Contrary to total nitrogen (TN), 

concentrations of TP and soluble reactive phosphorus (SRP) did not show a gradient with distance from 

land; however, TP was similarly higher during the wet season in areas receiving inputs from canals. TP in 

North Bay was significantly higher than the other regions at all times of the year. 

The highest median chlorophyll a concentrations were also found in the North Bay zone and lowest in 

South Bay. An earlier water quality study found similarly high chlorophyll a in North Bay (8.6 μg l-1) and 

low chlorophyll a in South Bay (0.2 μg l-1) (Brand 1998). Brand et al. (1991) also noted that the highest 

chlorophyll a concentrations were always associated with lower salinities, suggesting that the source of

nutrients generating phytoplankton blooms is freshwater runoff.

Table 7. Summary statistics for water quality in Biscayne Bay, 1994–2003, by season (all 

concentrations are mg l-1, except chlorophyll a, which is μg l-1) (Caccia and Boyer 2005).
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The FIU Coastal Water Quality Monitoring Network has collected water quality data monthly at 25 

stations in Biscayne Bay since fall 1993 (Boyer and Briceño 2008). Boyer and Briceño (2008) found 6 

groups of stations with similar water quality (Figure 8): the Alongshore group (AS), Inshore group (IS), 

main Bay group (MAIN), ocean channel group (not shown in Figure 8), Card Sound group (SCARD), and 

Turkey Point station, which comprised its own group (not shown in Figure 8).

The 2008 Cumulative Annual Report for the Coastal Water Quality Monitoring Network provides 

summary figures for each parameter by station group (Boyer and Briceño 2008). Figures 9 through 13

also show the long-term data for each of the parameters by group. In general, chlorophyll a, DIN, and 

TP concentrations were highest nearshore and decreased with distance away from shore, and North Bay 

had the highest DIN and TP concentrations. In most areas chlorophyll a was low and followed the same 

gradient as TP.

Waters on the 303(d) List

Table 8 provides the complete list of waters that are verified impaired in the Southeast Coast–Biscayne 

Bay Basin, and Table 9 identifies the waters that are proposed for delisting. See Appendix A for the 

Cycle 2 draft list of all verified impairments for both estuary and stream waters (FDEP 2010a, b). 
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Figure 8. Zones of similar water quality in Biscayne Bay (Boyer and Briceño 2008). 
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Figure 9. Box-and-whisker plots of water quality in the Alongshore zone (Boyer and Briceño 2008).
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Figure 10. Box-and-whisker plots of water quality in the Inshore zone (Boyer and Briceño 2008).
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Figure 11. Box-and-whisker plots of water quality in the Main Bay zone (Boyer and Briceño 2008).
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Figure 12. Box-and-whisker plots of water quality in the South Card zone (Boyer and Briceño 2008).
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Figure 13. Box-and-whisker plots of water quality in the North Bay zone (Boyer and Briceño 2008).
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Table 8. Waterbodies on the 2010 Verified List for impairments in Biscayne Bay (FDEP). 

IIIM = Class III Marine

IIIF = Class III Freshwater

Chla = Chlorophyll a

Basin 

Group 

Name

Planning 

Unit

Waterbody 

ID 

(WBID)

Waterbody 

Segment 

Waterbody 

Type

Waterbody 

Class1

Parameters 

Assessed 

Using 2001 

IWR

Concentration 

Causing 

Impairment2

Priority for 

TMDL 

Development3

Comments

(# Exceedances/# 

Samples)

PP = Planning Period 

VP = Verified Period4

Southeast 

Coast–

Biscayne 

Bay

Biscayne 

Bay 

Intracoastal

3226H ICWW 

(Miami-Dade 

County)

Estuary IIIM Fecal 

Coliform

>400 colonies/

100mL

Medium PP = 311/2525; 

VP = 218/1397

Southeast 

Coast–

Biscayne 

Bay

Broward 

County

3274 C-13 East 

(Middle River 

Canal)

Estuary IIIM Fecal 

Coliform

>400 colonies/

100mL

Medium PP = 19/168; 

VP = 39/205 

Data based on updated 

Run 22 from 10-26-05.

Southeast 

Coast–

Biscayne 

Bay

Broward 

County

3274 C-13 East 

(Middle River 

Canal)

Estuary IIIM Nutrients 

(Historic 

chla)

TN = 1.34 mg/L 

TP = 0.08 mg/L

Medium VP: Annual average chla

values in verified period 

exceeded historical 

minimum (of 2.5 μg/L for 

1992–96) by more than 

50% in 2001 (5.0825 μg/L), 

2002 (9.5931 μg/L), 2003 

(8.0321 μg/L) and 2004 

(8.1306 μg/L). Data 

indicate that WBID is colimited (TN/TP median = 

18.674, standard deviation 

15.003, range 4.96 to 

81.07, 71 observations). 

Data based on updated 

Run 22 from 10-26-05.

Southeast 

Coast–

Biscayne 

Bay

Broward 

County

3226G4 Las Olas Isles 

Finger Canal 

System

Estuary IIIM Fecal 

Coliform

>400 colonies/

100mL

Medium PP = 199/563; 

VP = 20/74 

Data based on updated 

Run 22 from 10-26-05.

Southeast 

Coast–

Biscayne 

Bay

Broward 

County

3276A New River 

(North Fork)

Estuary IIIM DO < 4.0 mg/L Medium PP = 28 / 86; 

VP = 28 / 83 Verified 

impaired and nutrients 

were found to be causative 
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Basin 

Group 

Name

Planning 

Unit

Waterbody 

ID 

(WBID)

Waterbody 

Segment 

Waterbody 

Type

Waterbody 

Class1

Parameters 

Assessed 

Using 2001 

IWR

Concentration 

Causing 

Impairment2

Priority for 

TMDL 

Development3

Comments

(# Exceedances/# 

Samples)

PP = Planning Period 

VP = Verified Period4

pollutant. Data based on 

updated Run 22 from 10-

26-05.

Southeast 

Coast–

Biscayne 

Bay

Broward 

County

3276A New River 

(North Fork)

Estuary IIIM Fecal 

Coliform

>400 colonies/

100mL

Medium PP = 147/265; 

VP = 45/104. 

Data based on updated 

Run 22 from 10-26-05.

Southeast 

Coast–

Biscayne 

Bay

Broward 

County

3276A New River 

(North Fork)

Estuary IIIM Nutrients 

(Chl a)

TN = 1.62 mg/L 

TP = 0.11 mg/L

Medium VP: Chla values exceeded 

IWR threshold in 1998 

(28.18 μg/L), 1999 (29.42 

μg/L), 2000 (16.3 μg/L), 

2001 (14.04 μg/L) and 

2004 (26.27 μg/L). Data 

indicate that WBID is colimited (TN/TP median = 

13.818, standard deviation 

8.7913, range 5.609 to 

62.0, 88 observations). 

Data based on updated 

Run 22 from 10-26-05.

Southeast 

Coast–

Biscayne 

Bay

Broward 

County

3276A New River 

(North Fork)

Estuary IIIM Total 

Coliform

>2,400 colonies/

100mL

Medium PP = 56/151; 

VP = 13/53 

Data based on updated 

Run 22 from 10-26-05.

Southeast 

Coast–

Biscayne 

Bay

Broward 

County

3277A New River Canal 

(South)

Estuary IIIM Fecal 

Coliform

>400 colonies/

100mL

Low PP = 23/184; 

VP = 22/144 

Data based on updated 

Run 22 from 10-26-05.

Southeast 

Coast–

Biscayne 

Bay

Broward 

County

3277A New River Canal 

(South)

Estuary IIIM Nutrients 

(Historic Chl 

a)

TN = 1.84 mg/L 

TP = 0.07 mg/L

Low VP: Annual average chla

values in verified period 

exceeded historical 

minimum value (of 4.8 

μg/L for 1995–99) by more 

than 50% in 2003 (7.9892 

μg/L) and 2004 (7.2405 

μg/L). Data indicate that 
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Basin 

Group 

Name

Planning 

Unit

Waterbody 

ID 

(WBID)

Waterbody 

Segment 

Waterbody 

Type

Waterbody 

Class1

Parameters 

Assessed 

Using 2001 

IWR

Concentration 

Causing 

Impairment2

Priority for 

TMDL 

Development3

Comments

(# Exceedances/# 

Samples)

PP = Planning Period 

VP = Verified Period4

WBID is co-limited (TN/TP 

median = 29.521, standard 

deviation 50.263, range 

7.337 247.9, 94 

observations). Data based 

on updated Run 22 from 

10-26-05.

Southeast 

Coast–

Biscayne 

Bay

North Dade 

County

3288 C-6/Miami River Estuary IIIM Copper > 3.7 μg/L Medium PP = 18/69; 

VP = 14/46

Southeast 

Coast–

Biscayne 

Bay

North Dade 

County

3288 C-6/Miami River Estuary IIIM Fecal 

Coliform

>400 colonies/

100mL

Low PP = 253/631; 

VP = 202/434

Southeast 

Coast–

Biscayne 

Bay

North Dade 

County

3288 C-6/Miami River Estuary IIIM Total 

Coliform

>2,400 colonies/

100mL

Low PP = 191/629; 

VP = 152/432

Southeast 

Coast–

Biscayne 

Bay

North Dade 

County

3290 C-6/Miami River Estuary IIIF Fecal 

Coliform

>400 colonies/

100 mL

Medium PP = 27/167; 

VP = 33/149

Southeast 

Coast–

Biscayne 

Bay

North Dade 

County

3288A Wagner Creek Estuary IIIM Dioxin >7 ppt Medium Verified impaired based on 

fish advisory for checkered 

puffer, striped majarra, 

and yellow fin mojarra.

Southeast 

Coast–

Biscayne 

Bay

North Dade 

County

3288A Wagner Creek Estuary IIIM Fecal 

Coliform

>400 colonies/

100mL

High PP = 198/223; 

VP = 139/157

Southeast 

Coast–

Biscayne 

Bay

North Dade 

County

3288A Wagner Creek Estuary IIIM Total 

Coliform

>2,400 colonies/

100mL

High PP = 193/223; 

VP = 137/157
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Basin 

Group 

Name

Planning 

Unit

Waterbody 

ID 

(WBID)

Waterbody 

Segment 

Waterbody 

Type

Waterbody 

Class1

Parameters 

Assessed 

Using 2001 

IWR

Concentration 

Causing 

Impairment2

Priority for 

TMDL 

Development3

Comments

(# Exceedances/# 

Samples)

PP = Planning Period 

VP = Verified Period4

Southeast 

Coast–

Biscayne 

Bay

North Dade 

County

3288B C-6/Miami River 

(Lower Segment)

Estuary IIIM Fecal 

Coliform

>400 colonies/

100mL

Medium PP = 38/74; 

VP = 16/26

Southeast 

Coast–

Biscayne 

Bay

North Dade 

County

3288B C-6/Miami River 

(Lower Segment)

Estuary IIIM Total 

Coliform

>2,400 colonies/

100mL

Medium PP = 31/73; 

VP = 15/26
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Table 9. Estuarine waterbodies in Biscayne Bay that are proposed for delisting (FDEP).

Chla = Chlorophyll a

IIIM = Class III Marine

Basin 

Group 

Name

Planning 

Unit

WBID Waterbody 

Segment

Waterbody Type Waterbody 

Class

1998 303(D) 

Parameters of Concern

Parameters 

Evaluated Using 

IWR

Comments 

(with # of Exceedances/

# of Samples

Southeast 

Coast–

Biscayne 

Bay

Broward 

County

3282 Hollywood Canal Estuary IIIM Nutrients Nutrients (Chl a) Chla values exceeded IWR threshold 

in 1998 (22.74 μg/L), but annual 

average chla values did not exceed 

IWR threshold of 11.0 μg/L in 1999 

(10.4 μg/L), 2000 (4.123 μg/L), 2001 

(7.063 μg/L), 2002 (5.623 μg/L) and 

2004 (4.51 μg/L). TN (1.0295 mg/L) 

exceeds threshold of 1.0 mg/L. TP 

(0.0625 mg/L) does not exceed 

screening threshold of 0.19 mg/L. 

Data based on updated Run 22 from 

10-26-05. 

Southeast 

Coast–

Biscayne 

Bay

Broward 

County

3277A South New River 

Canal

Estuary IIIM Nutrients Nutrients (Chl a) Annual average chla values do not 

exceed IWR threshold of 11.0 μg/L in 

1998 (4.177 μg/L), 1999 (4.597 μg/L), 

2000 (5.326 μg/L), 2001 (7.486 μg/L), 

2002 (3.28 μg/L), 2003 (7.989 μg/L) 

and 2004 (7.241 μg/L). TN (1.5835 

mg/L) exceeds screening threshold of 

1.0 mg/L. TP (0.051 mg/L) does not 

exceed screening threshold of 0.19 

mg/L. Data based on updated Run 22 

from 10-26-05. 

Southeast 

Coast–

Biscayne 

Bay

Broward 

County

3277A South New River 

Canal

Estuary IIIM Coliforms Total Coliform PP = 6/146; 

VP = 8/93 

Data based on updated Run 22 from 

10-26-05. Not impaired.
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Proposed Numeric Nutrient Targets 

FDEP recommends regionalizing the bay into sub-basins with similar water quality characteristics and 

applying the “maintain existing conditions” approach to setting nutrient criteria. FDEP proposes 

preliminary criteria calculated using long-term water quality data collected from 1995 to 2009 by FIU.

Regionalization 

FIU has used the data collected as part of its 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 FIU have 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 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 used a longer period of record and a modified set of 

parameters. The analysis, which 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 Table 10 

and Figure 14. Appendix A provides more detail on the analysis conducted by Henry Briceño, Joe Boyer, 

and Peter Harlem from FIU. 

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 TP, TN, and 

chlorophyll a. 

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

those of Biscayne Bay, were divided as detailed in Table 10 and illustrated in Figure 14. Table 10 lists the

sub-basins for Biscayne Bay. 

Table 10. Proposed regionalization for Biscayne Bay. 

Sub-Basin Map Code Sub-Basin Name

MBS Manatee Bay-Barnes Sound

SCO South Central Outer-Bay

SCI South Central Inshore

SCM South Central Mid-Bay

CS Card Sound

SNB Southern North Bay

NCI North Central Inshore

NCO North Central Outer-Bay
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Draft 29 August 2010

Figure 14. Proposed estuarine and coastal nutrient criteria sub-basins for south Florida.
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Draft 30 August 2010

Proposed Numeric Criteria 

To be applied consistently and to provide 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 a pollutant may be above the magnitude, and frequency relates to how often the 

magnitude may be exceeded without adverse effects. It is preferable to derive the magnitude 

component of a criterion through a cause-effect relationship (such as that 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 sufficient data to demonstrate a cause-effect 

relationship, the magnitude may be set at a level designed to maintain the current data distribution, 

accounting for natural temporal variability, assuming 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 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 magnitude component can be set at the long-term central tendency (geometric mean) of 

the distribution, while the frequency and duration components describe how often and by how much 

nutrient concentrations can be above the central tendency while still being consistent with the 

reference distribution. The derivation of the magnitude, frequency and duration components of 

numeric nutrient criteria for the Southwest Coastal area 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 (Appendix B). 

Magnitude

The magnitude component represents a level of nutrients demonstrated to be protective of the 

designated use. For the “healthy existing conditions” approach, the magnitude can be interpreted as 

the central tendency of the baseline distribution and may be set at a level that represents a long-term 

average condition of that distribution. The long-term average condition may also be 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 referencebased approach fails to identify a threshold of imbalance, and thus is highly prone to excessive Type I 

error. For the purpose of antidegradation evaluations, the U.S. Environmental Protection Agency (EPA) 

has historically considered a 10% change in a water quality parameter to represent an insignificant 

departure from the existing condition. Therefore, the magnitude component of the criteria was derived 

based on a 10%increase in the long-term geometric mean calculated as the geometric mean of the 

annual geometric means from the long-term existing dataset for each sub-basin area identified above.

Frequency and Duration

To provide a consistent and appropriate level of protection, the duration and frequency components of 

the criteria must be consistent with the derivation of the magnitude component. While the magnitude 
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Draft 31 August 2010

component of the criteria is being expressed as a long-term geometric mean concentration, in most 

cases based on 9 or more years of data, it is not practical to assess compliance with the criteria on the 

same long-term basis. Instead, a statistical test can be developed to allow the application of the criteria 

on a shorter-term basis. For the criteria to be protective, the duration component of the criteria (e.g., 

single sample maximum, annual geometric mean) must be linked to the response time frame 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 time frames. If, however, such a short-term response cannot be 

demonstrated, or there is no indication of use impairment, then longer averaging periods should be 

considered. 

For example, since the relationship between nutrient and chlorophyll a response in Florida lakes was

extremely weak, with a much more robust relationship found when data were evaluated based on 

annually averaged log-transformed data, FDEP and EPA used an averaging period of a year to assess the 

enrichment in Florida lakes with the criteria being expressed as an annual geometric mean. Likewise, 

the nutrient criteria for estuaries will be assessed annually. Since the duration and frequency 

components of the criteria must be consistent with the derivation of the magnitude component to 

provide a consistent and appropriate level of protection, the long-term geometric mean target cannot 

simply be applied as an annual mean. Doing so would result in unacceptably high Type I failure rate 

(identifying a healthy system as being impaired), since approximately 50% of the individual years can be 

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 10%. 

An annual target concentration with an approximate 10% Type I error rate for a given frequency can be 

derived by appropriately accounting for the annual variability above the mean. This annual target 

concentration can be derived as an upper percentile of the distribution of the annual geometric mean 

concentrations. Previous proposals by EPA have used 3-year assessment periods to express the 

magnitude and duration nutrient criteria components. Although it is possible to construct a test that 

achieves the 10% Type I error rate target, a slightly longer period (e.g., 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 3 years in Florida (and may actually be on a multidecadal scale). Furthermore, a 5-year 

period is more consistent with both the state’s 5-year 303(d) assessment and permit renewal cycles.

Assuming a 5-year assessment period, it can be statistically determined that using the 75th percentile of 

the annual geometric means from the long-term dataset with a frequency and duration of no more than 

twice during the 5-year period will achieve the targeted 10% error rate. Therefore the proposed criteria 

will be applied such that the 75th percentile of the annual geometric mean concentrations cannot be 

exceeded in more than 2 out of 5 years.

Summary of the Proposed Criteria

FDEP proposes that the magnitude component of protective nutrient criteria be expressed as a longterm geometric mean concentration target, derived as the geometric mean of the annual geometric 

mean concentrations from the long-term baseline dataset plus a 10% increase, which the EPA considers 

to be insignificant. The duration component of the criteria would be a 1-year assessment period, with 

the annual target being expressed as the 75th percentile for the geometric mean target based on a lognormal distribution. Finally, the frequency component of the criteria would be expressed as the annual 

target cannot be exceeded in more than 2 out of 5 years. The frequency and duration components were 

designed to assess whether the interannual variability is consistent with the maintenance of the long-
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Draft 32 August 2010

term mean, considering natural variability around that mean. If the frequency and duration 

components of the criteria are satisfied, it can be concluded, with a known level of statistical certainty, 

that the long-term target is also being achieved.

In simpler terms, the criterion would be expressed as a long-term geometric mean nutrient 

concentration target derived as the long-term geometric mean nutrient concentration plus 10%. The 

criteria would be applied such that the observed annual geometric mean nutrient concentration cannot 

exceed the annual target more than 2 out of 5 years, with the annual target being derived as the 75th

percentile of the long-term geometric mean target concentration.

Tables 11 through 13 provide the proposed long-term targets as well the annual limits for each subbasin in Biscayne Bay. The next step in finalizing the proposed criteria is to evaluate the similarities 

among the different sub-basins to determine if any of the sub-basins could be combined in respect to 

criteria development. The process of evaluating the similarities among sub-basins is currently under

way, and the results will be provided once the analysis has been completed.

Table 11. Proposed numeric nutrient criteria for all segments of the Biscayne Bay, 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) 

Existing 

Long Term 

Geometric 

Mean

Maximum 

Allowed Long 

Term Geometric 

Mean

Annual Geometric Mean 

for a Network of 

Stations (2 of 5 year 

exceedence rate)

Annual Geometric 

Mean for a Single 

Site (2 of 5 year 

exceedance rate)

Manatee Bay-Barnes 

Sound 6.90 7.59 10.13 10.28

South Central Outer-Bay 5.20 5.72 6.69 6.88

South Central Inshore 5.88 6.47 7.70 7.90

South Central Mid-Bay 5.31 5.84 7.06 7.31

Card Sound 5.90 6.49 7.87 8.04

Southern North Bay 7.86 8.65 9.98 10.19

North Central Inshore 5.59 6.15 7.49 7.62

North Central Outer-Bay 6.35 6.98 8.13 8.30

Northern North Bay 9.86 10.84 12.22 12.45

Total Nitrogen (μg l-1) 

Existing 

Long Term 

Geometric 

Mean

Maximum 

Allowed Long 

Term Geometric 

Mean

Annual Geometric Mean 

for a Network of 

Stations (2 of 5 year 

exceedence rate)

Annual Geometric 

Mean for a Single 

Site (2 of 5 year 

exceedance rate)

Manatee Bay-Barnes 

Sound 459 505 588 602

South Central Outer-Bay 190 209 250 259
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South Central Inshore 391 430 504 518

South Central Mid-Bay 282 310 365 371

Card Sound 257 283 350 370

Southern North Bay 231 254 299 304

North Central Inshore 247 272 325 329

North Central Outer-Bay 221 243 286 289

Northern North Bay 235 259 310 315

Chlorophyll a (μg l

-1) 

Existing 

Long Term 

Geometric 

Mean

Maximum 

Allowed Long 

Term Geometric 

Mean

Annual Geometric Mean 

for a Network of 

Stations (2 of 5 year 

exceedence rate)

Annual Geometric 

Mean for a Single 

Site (2 of 5 year 

exceedance rate)

Manatee Bay-Barnes 

Sound 0.50 0.55 0.89 0.91

South Central Outer-Bay 0.21 0.23 0.27 0.31

South Central Inshore 0.28 0.31 0.38 0.39

South Central Mid-Bay 0.25 0.28 0.34 0.36

Card Sound 0.34 0.37 0.52 0.55

Southern North Bay 0.85 0.93 1.10 1.15

North Central Inshore 0.32 0.36 0.46 0.50

North Central Outer-Bay 0.49 0.54 0.72 0.79

Northern North Bay 1.41 1.55 1.81 1.86
Nutrient Criteria Technical Support Document Biscayne Bay

Draft 34 August 2010

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Nutrient Criteria Technical Support Document Biscayne Bay

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Appendix A. Impaired Waters in the Biscayne Bay Basin
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Draft 39 August 2010
Nutrient Criteria Technical Support Document Biscayne Bay

Draft 40 August 2010
Nutrient Criteria Technical Support Document Biscayne Bay

Draft 41 August 2010
Nutrient Criteria Technical Support Document Biscayne Bay

Draft 42 August 2010

Appendix B: Overview of FDEP Approaches for Nutrient Criteria Development in Marine 

Waters

To be inserted.