# Site

- Specific Information in Support of Establishing Numeric Nutrient
Criteria for Choctawhatchee Bay

Florida Department of Environmental Protection Tallahassee, FL 32399

August 13, 2010Draft ii July 2010 

### Table of Contents

Executive Summary

............................................................................................................... 1
Geographic and Physical Description

..................................................................................... 4

Sources and Fates of Nutrients

.............................................................................................. 7
Biological Summary

............................................................................................................... 8

Seagrasses in Choctawhatchee Bay

................................................................................................ . 8
Tidal Marshes in Choctawhatchee Bay

.......................................................................................... 15
Phytoplankton

.............................................................................................................................. 17

Invertebrates

............................................................................................................................... 18
Fisheries in Choctawhatchee Bay

.................................................................................................. 22
Shellfish Harvesting

...................................................................................................................... 25
Red Tide and Associated Animal Mortality Events

......................................................................... 26 

### Water Quality Studies

......................................................................................................... 27 CBA Partnership with University of Florida LakeWatch/Project COAST Program

............................. 27 CBA/Okaloosa

- Walton College Long

- Term Sampling and Data Coordination

.................................. 28
FDEP Water Quality Analyses

........................................................................................................ 32 

### Waters on the 303(d) List

..................................................................................................... 36

Num eric Nutrient Criteria Recommendation

........................................................................ 37
Relationship between Anthropogenic Nutrient Inputs and Adverse Biological Effects

..................... 37
Proposed Numeric Nutrient and Chlorophyll Criteria

...................................................................... 38Draft iii July 2010 

### List of Tables

Table 1a. Checklist of nutrient enrichment symptoms in Choctawhatchee Bay

.......................................... 2
Table 1b. Checklist of additional environmental factors in Choctawhatchee Bay

....................................... 3
Table 2. Choctawhatchee Bay physical char acteristics.

............................................................................... 6
Table 3. Choctawhatchee Bay seagrass status, 1992 (from Ruth and Handley 2002).

............................. 11
Table 4. Vascular plants from Hogtown Bayou tidal marshes (from Keppner and Keppner 2003).

.......... 15
Table 5. Benthic macroinvertebrates reported from Choctawhatchee Bay (after Foster 2000 and Fox et al. 2001).

........................................................................................................................ 19
Table 6. In 1993, a total of 513,517 organisms, representing 108 taxa, were collected.

.......................... 23

Table 7. 1994 Fixed

- station sampling yielded 459,835 organisms representing 117 taxa.

....................... 24
Table 8. 1995 fixed

- station sampling yielded 470,763 organisms representing 105 taxa.

........................ 24
Table 9. 1996 stratified random sampling by seine and trawl yielded 462,945 organisms representing 711 taxa.

.............................................................................................................. 25
Table 10. Summary of the spatial water chemistry analyses from six sections along the horizontal length of the Choctawhatchee Bay. Section 1 is located along the east side of t he bay near the Choctawhatchee River. Section 6 is located along the west side of the bay near East Pass. Small letters next to each mean represent statistically significant differences (Terrell 2010).

....................................................................................... 30

Table 11

. Temporal water chemistry analyses over a 40

- year period of record, 1968

– 2007 (Terrell2010).

............................................................................................................................ 31 Table 12. Summary of the spatial water chemistry analyses for three sections (based on surface salinity) along the horizontal length of Choctawhatchee Bay, 2000

– 09. Small letters next to each mean represe nts statistically significant differences (Lazzarino and Terrell 2010).

............................................................................................................................. 31
Table 13. Summary of data analysis for Choctawhatchee Bay, all stations combined, 1996

– 2009.

......... 32
Table 14. Mean surface and bottom turbidity for Choctawhatchee Bay salinity

- based regions

, 2000

– 09 (from Lazzarino and Terrell 2010).

............................................................................. 36
Table 15. Waterbodies in the Choctawhatchee Bay Planning Unit proposed for DELISTIN G from the 1998 303(d) list for either nutrients or DO (FDEP 2010b).

.................................................. 36
Table 16. Proposed numeric nutrient criteria for all segments of Choctawhatchee 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.

......................................................................................................................... 40Draft iv July 2010 

### List of Figures

Figure 1. Map of Choctawhatchee Bay and adjacent urban areas and land management areas.

............. 5
Figure 2. Location of Choctawhatchee Bay watershed and estuary (Schaeffer 2010).

............................... 6
Figure 3. Land uses in the Choctawhatchee Bay watershed, with areal coverages and percentages of total area (from Schaeffer 2010).

...................................................................... 7
Figure 4. Choctawhatchee Bay segments for seagrass mapping study.

.................................................... 11
Figure 5. Seagrass coverage in Choctawhatchee Bay, 1992.

..................................................................... 13
Figure 6. Choctawhatchee Bay seagrass coverage comparison, 1992 and 2003 (Alexander 2010).

......... 14
Figure 7. Western Choctawhatchee Bay seagrass coverage comparison, 1992 and 2003 (Alexander 2010).

...................................................................................................................... 14
Figure 8. Location of Hogtown Bayou study area for vascular plant inventory and invertebrate sampling (Keppner and Keppner 2003).

................................................................................... 17
Figure 9. Location of Choctawhatchee Bay biological sampling stations, 1985

– 98 (Livingston 2010).

................................................................................................ ........................................ 19
Figure 10. Phytoplankton cell numbers and species richness at mid

- bay stations in Choctawhatchee Bay and East Pass Lagoon (Station 36e), averaged from monthly data, September 1985

– August 1995 (Livingston 2010).

.......................................................... 20
Figure 11. Phytoplankton bloom numbers at mid

- bay stations in Choctawhatchee Bay and East Pass Lagoon (Station 36e), averaged from monthly data, September 1985

– August 1995 (Livingston 2010).

............................................................................................................ 21
Figure 12. Total numbers of infauna and fish, averaged from monthly data from September

1985

– August 1995 (Livingston 20 10).

...................................................................................... 22
Figure 13. Choctawhatchee Bay is located in the Panhandle region of Florida, within Okaloosa and Walton Counties (top). Cu rrently, the CBA samples almost 90 stations sampled monthly throughout Choctawhatchee Bay (bottom). Each red dot is a sampling

station.

................................................................................................ ...................................... 28
Figure 14. Trend of annual geometric means for TP in Choctawhatchee Bay, 1996

– 2009, and long

- term geometric mean.

...................................................................................................... 33
Figure 15. Trend of annual geometric means for TN in Choctawhatchee Bay, from IWR dataset,

1996

– 2009, and long

- term geometric mean.

........................................................................... 33

Fi gure 16. Trend of annual geometric means for chlorophyll a in Choctawhatchee Bay, from IWR dataset, 1996

– 2009, and long

- term geometric mean.

............................................................. 34
Figure 17. Comparison of annual geometric means for TP for Choctawhatchee Bay regions based on salinity, from IWR dataset, 1996

– 2009.

.............................................................................. 34
Figure 18. Comparison of annual geometric means for TN for Choctawhatchee Bay regions based on salinity, from IWR dataset, 1996

– 2009.

.................................................................... 35
Figure 19. Comparison of annual geometric means for chlorophyll a for Choctawhatchee Bay regions based on salinity, from IWR dataset, 1996

– 2009.

....................................................... 35Draft 1 July 2010 

### Executive Summary

This report was prepared by t he Florida Department of Environmental Protection (FDEP), in cooperation with local scientists, to support the development of numeric nutrient criteria for Choctawhatchee Bay. The primary purpose of the proposed numeric nutrient criteria is to protect healt hy

, well

- balanced natural populations of flora and fauna from the effects of excess nutrient enrichment.

Choctawhatchee Bay is a large estuary aligned along an east

- west axis with a major alluvial river basin ( the Choctawhatchee River) at the east end and a gulf pass (East Pass) in the western region. Freshwater input is largely from the Choctawhatchee River, with secondary inflows from a series of bayous located primarily in the northern sections of the bay. The estuary was originally oligohaline, and

seawater entered the system only through periodic breaks in the barrier islands (Hemming and Brown 2004; Morang 1992)

. In response to dredging the pass in 1929 , a strong halocline and subsequent hypoxia developed , and a layer of “liquid mud” formed in the benthic zone (Livingston 1987; Ruth and Handley 2002).

The primary source s of nutrient loading to the estuary are the Choctawhatchee River and secondary
inflows

. O ther sources of nutrients include 5 point sources to surface waters (in the Choctawhatchee Bay Planning Unit) , nonpoint sources (stormwater runoff and septic tanks), natural inputs (leaf litter), atmospheric deposition, and ground water.

Seagrass beds and tidal marshes are the primary productive habitats in Choctawhatchee Bay, and both
have ex perienced significant historic al losses in the system, particularly in the western portion of the bay. The causes of the seagrass and marsh loss are largely unknown, but suspected factors are the physical changes to the system that f ollowed increased sali nity in the system. Water quality studies indicate nutrient and chlorophyll concentrations throughout the bay are relatively low and do not appear to be limiting seagrass or tidal marsh growth and recovery

. Although the b iological resources of the bay ha ve ch ange d due to physical and salinity modifications

, the data indicate that nutrients are not currently problematic, and therefore the control of nutrient inputs would not improve biological condition. FDEP therefore recommends setting numeric nutrient criteria at current (1996

– 2009) levels

.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 2 July 2010 Table 1a. Checklist of nutrient enrichment symptoms in Choctawhatchee Bay

- - E mpty cell/no data N/A = Not applicable Response Variable Observed Historically? Observed Currently? Explanation Source

Low dissolved oxygen (DO) (hypoxia/anoxia) Yes Yes Yes, associated with strong halocline that developed following opening of East Pass and continues currently. Seasonal hypoxia in certain bayous and lagoons. Livingston 1986, 2010; Ruth and Handley 2002

Reduced clarity Yes Yes High turbidity and color are associated with high flow in the Choctawhatchee River. The layer of highly organic fine sediments (“liquid mud”) reduces clarity and contributes to low DO. Livingston 2010; U.S. Air Force (USAF) 1996

Increased chlorophyll a concentrations Yes No Ch lorophyll a concentrations are generally low in all regions of the bay. Historic increases (1967

- 2007) in eastern sections of bay. STORET (I mpaired Surface Waters Rule [I WR ] ) data; CBA data Phytoplankton blooms

(nuisance or toxic) Yes Episodic Episodic Karenia brevis blooms; diatom blooms in Destin Harbor (1986

– 88 ); diatom bloom in Chula Vista Bayou (2006); episodic presence of harmful species but not in bloom numbers. Florida Fish and Wildlife Conservation Commission (FWCC) Fish and Wildlife
Research I nstitute (FWRI) http://research.myfwc.com/features /category_main.asp?id=2309 ; Livingston 2010 Problematic epiphyte growth No No No problematic epiphytic growth has been reported ; however, detailed
studies of epiphytes on seagrass es in Choctawhatchee Bay have not
been conducted. -

Problematic macroalgal growth No No No problematic macroalgal growth has been reported for the system; records of macroalgae in the system were not found. -

Submerged aquatic

vegetation (SAV) community changes or loss Yes Yes Anecdotal evidence for decline of fresh and brackish macrophytes following opening of East Pass, due to subsequent salinity changes.

Loss of saltwater SAV has continued, although estimates vary. Decreased transparency (due to turbidity) is a likely cause. Halodule beds in Hogtown Bayou are healthy. Burch 1983; USAF 1996; Ruth and Handley 2002; Livingston 2010

Emergent vegetation community changes or loss Yes No Anecdotal evidence for decline of tidal marshes following opening of East Pass and subsequent salinity changes. Compared with other Gulf estuaries, there is little emergent vegetation, but reasons are unclear. USAF 1996; Livingston 2010

Coral/hardbottom community changes or loss N/A N/A - -

Impacts to benthic community Yes Yes Low productivity in infaunal and epibenthic communities compared with other regional Gulf estuaries; salinity stratification and high organic silts (resulting in low DO), are contributing factors. Livingston 2010; USAF 1996

Fish kills Yes Episodic Primarily related to Karenia brevis blooms FWR I http://research.myfwc.com/fishkill/Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 3 July 2010 Other - - - -

Table 1b. Checklist of additional environmental factors in Choctawhatchee Bay

Factors Observed? Explanation Source Increased nutrient loading or concentrations from
historical levels No CBA analyzed a combined dataset (1968

– 2007), to study temporal trends. No significant increases in concentrations, except for TN in NWFWMD Segment 4 (corresponds to portion of “Middle CB” segment used by CBA
and FD EP). Terrell 2010

Mitigating factors that could prevent nutrient expression Yes Turbidity, color Terrell 2010

Other significant stressors to biological
communities Yes Salinity stratification and associated hypoxia; layer of organic fine
sediments ref erred to as “liquid mud”; turbidity from Choctawhatchee River; poor flushing. Livingston 2010

Natural episodic events contributing to nutrient regime ( e.g., seasonal or hydrologically driven) Yes Choctawhatchee River flow a major controlling factor of nutrient and
sediment loads. Schaeffer 2010; Livingston 2010Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 4 July 2010 

### Geographic and Physical Description

Choctawhatchee Bay is a large estuary in Okaloosa and Walton Count ies , Florida, with a length of 43 kilometers ( km ) , and a width varying between 2 and 10 km

. The surface area of the bay is approximately 348 square kilometers ( km2 )

. The bay is aligned along an east

- west axis, with a major

alluvial river basin, the Choctawhatchee River, at the eastern end. A small but influential pass to the

Gulf of Mexico (East Pass) is in the western region, immediately west of De stin (Livingston 2010)

. The bay has shallow shelf areas and relatively steep slopes that eventually level out to average depths of 3

meters in eastern sections and 8 meters in weste rn sections (Livingston 2010).

The Choctawhatchee River provides approximately 90% of the freshwater input to the bay system, with secondary inflows from a series of bayous located mainly in the northern sections of the bay. The r iver has a broad floodplain and floods seasonally. It is the fourth longest river in Florida and the third largest

in terms o f discharge (Fernald and Purd um 1998 ; Schaeffer 2010), with a n annual average discharge rate

of 243 cubic meters per second ( m 3 s -1 ) (8,580 ft 3 s -1 ) (Northwest Florida Water Management District
[NWFWMD] 1996)

. Major tributaries of the Choctawhatchee River include the Pea and Little Choctawhatchee Rivers, and Holmes, Wrights, Bruce, and Pine Log creeks (NWFWMD 2002). Other

sources of fresh water to the bay include many small creeks and ba yous that drain directly to the bay

, the most significant being Turkey, Rocky, Swift , and Alaqua Creek s. There are 13 Floridan aquifer springs

in the Choctawhatchee River B asin that contribute clear, alkaline water. Rainfall, surficial ground water, and overland flow also contribute significant amounts of fresh water to the estuary (USAF 1996)

. Average n et precipitation in the system is estimated at 50 inches per year (Blaylock 1983)

. Historically, marine waters entered the bay only through periodic breaks in the barrier islands (Hemming

and Brown 200 4 ). However, an artificial channel, East Pass , was opened in 1929 to provide a permanent pass through the previously intermittent opening. The opening of East Pass resulted in increased salinity and the subsequent loss of marshes, swamps, and seagrass beds throughout the bay (Livingston

2010; Ruth and Handley 2002 ). The bay opens to the Gulf Intracoastal Waterway (GIWW) in the east

, connecting Choctawhatchee Bay to West Bay ( of the St. Andrew s system)

. In the west, t he bay opens to

Santa Rosa Sound and the GIWW, connecting Choctawhatchee Bay to the Pensacola Bay system (Blaylock 1983). The GIWW is regularly maintained by the U.S. Army Corps of Engineers. Pensacola Pass is separated from th e west side of the bay by an 84

- km ( 52

- mi le ) portion of the GIWW that was initially dredged in the 1940s (NWFWMD 1996).

Choctawhatchee Bay is a highly stratifi ed system with minimal tidal ex c hange (tidal range is 0.15 m).
Water exchange with the Gulf of Mexico is limited to the narrow, shallow East Pass (Blaylock 1983;

Li vingston 1986; USAF 1996 ). The strong halocline ( a noticeable change in salt concentrations between

surface waters and deeper waters) is due to reduced tidal mixing (Blaylock 1983; Collard 1976 ), and

h ypoxia is a c ommon and persistent phenomenon due to the vertical stratification. The significant

freshwater influence from the Choctawhatchee River

, accompanied by the influx of salt water from the
Gulf of Mexico, causes salinity fluctuation and stra tification

. Sali nities range from 0 to 34 parts per thousand (ppt) on an east

- to

- west gradient

, from the river delta to th e East Pass opening to the Gulf

. Water temperatures range from 13.7  ̊ to 19.8 °C

, with peak temperatures generally occurring in July and
August

, and the lowest temperatures in December and January. The pH in the bay ranges from 7.0 toNutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 5 July 2010 8.1 standard units ( SU ) . Depths range from 3 to 13 m, with a mean depth of 3.8 m (Schaeffer 2010). The bay has shallow shelf areas and relatively steep slopes that eventually level out to average depths of

3 m in eastern sections and 8m in western sections (Livingston 2010). Table 2 summarizes the bay’s

p hysical characteristics.

Much of the watershed i n the vicinity of Choctawhatchee Bay is publicly owned, including Rocky Bayou

State Park and managed areas within Eglin Air Force Base. Large portions of the bay are Class II w aters (app roved for shellfish harvesting)

. The easternmost part of the bay and the river delta, as well as Rocky Bayou State Park Aquatic Preserve, are designated as Outstanding Florida Waters (OFWs) ( Rule 62

- 302.700, Florida Administrative Code [F.A.C.] ), worthy of special protection because of their natural

attributes. Figure 1 contains a map of Choctawhatchee Bay showing major urban centers and publicly owned land management areas.

The bay has four basic natural habitats: shallow slope areas (vegetated, unvegetated, and oyster beds), deep central basin regions (unvegetated), bayous, and a river delta area.

Figure 1

. Map of Choctawhatchee Bay and adjacent urban areas and land management areas.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 6 July 2010 Table 2. Choctawhatchee Bay physical characteristics. Physical Characteristic Values Source Estuarine surface area (km 2 ) 348 km2 Florida Marine Research Institute ( FMRI ) 1993 Watershed area (km 2 ) 13x103 km2 Schaeffer 2010

Land use See Figure 3 Schaeffer 2010 Mean depth (m) 3.8 m Schaeffer 2010

Tidal range (m) 0.15 m Ruth and Handley 2002 Salinity and salinity zones 0- 34% Strong halocline FMRI 1993

Choctawhatchee Bay Basin

The Choctawhatchee Bay Basin encompasses nearly 13,856 km 2 (5,350 square miles [ mi 2] ) and spans portions of northwest Florida and south Alabama ( Figure 2 ). Approximately 42% of the basin is in north
Florida, with the rest in rural portions of south Alabama. Much of the watershed is composed of forest, agricultural , and rural land uses , with a large portion of the basin in Florida part of Eglin A ir Force Base ( Figure 3 ). Figure 3 also sh ows t he areal extent of each land use type and percentage of the total

watershed area. In addition, the watershed contains a portion of the sandhill lakes area of Washington
County.

Figure 2

. Location of Choctawhatchee Bay watershed and estuary (

Schaeffer 2010 ).Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 7 July 2010 Figure 3. L and uses in the Choctawhatchee Bay watershed, with areal coverages and percentages of total area (from Schaeffer 2010 ).



### Sources and Fates of Nutrients

Sources of nutrients to Choctawhatchee Bay include the Choctawhatche e River, numerous small creeks and bayous that drain directly to the bay, p oint source discharges, nonpoint source inputs (septic tanks
and stormwater from urban and agricultural areas), natural inputs ( plant leaf litter), and atmospheric deposition.

For FDEP water quality assessment purposes, t he Choctawhatchee Bay watershed is divided into the Pea River, Choctawhatchee River, and Choctawhatchee Bay Planning Units

. There are no permitted
domestic or industrial wastewater facilities in the Pea River Plan ning Unit , and only 1 closed landfill.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 8 July 2010 There are 20 permitted domestic wastewater facilities and 4 industrial facilities in the Choctawhatchee

River Planning Unit . Four of the permitted domestic wastewater facilities (Chipley, Bonifay, Graceville,
and No ma) discharge directly into surface waters, and a fifth (Vernon) discharges into percolation ponds
that overflow into surface waters. These facilities are concentrated in the Holmes Creek watershed (FDEP 2006) . There are also 12 permitted wastewater disc harges that do not discharge directly to
surface waters. T he Choctawhatchee River Planning Unit contains 11 landfills , 5 of which are active.
There is also 1 delisted Superfund site. The Pea River and Choctawhatchee River watersheds largely depend on on site sewage treatment and disposal systems (OSTDS, or septic tanks ) for the treatment and disposal of wastewater (NWFWMD 2002).

There are 5 permitted wastewater facilities in the Ch octawhatchee Bay Planning Unit with direct discharge to surface water. T hree of these are concrete batch plants, w hile the remaining 2 are indu strial waste facilities. An additional 25 permitted facilities (21 domestic waste and 4 industrial waste) have no direct surface wate r discharge but instead handle plant effluent in reuse systems. There are 18 landfills in the planning unit, 6 of which are active. Several areas in the vicinity of Choctawhatchee Bay rely substantially on OSTDS for the treatment and disposal of wastewat er (Knight and Wallman 2007) , although initiatives to extend sewer service into areas near the bay are ongoing.

Approximately 78 % of the land area in the Choctawhatchee Bay Planning Unit is composed of upland forest and wetlands. Approximately 12.5 % of the land area is urban and built

- up, primarily in the coastal area of the watershed. These human land uses can be associated with nonpoint discharges of pollutants
and eroded sediments. This s tormwater r unoff en ters Choctawhatchee Bay through the
Cho ctawhatchee River ; through numerous bayous, creeks, and ditches ; and as overland sheet flow.

Stormwater runoff is a potential threat to water quality in the b ay, delivering suspended sediments,

nutrients , and

, potentially, pesticides to the estuary. Esti mates of natural sources of nutrient inputs such as leaf litter remain unquantified.

A tmospheric deposition data for the watershed are available from the National Atmospheric Deposition Program’s Nati onal Trends Network (NADP

- NTN), which has a collection site in Sumatra, Florida (FL 23)

. Based on its loading data for the most recently reported year (2008), the NTN estimates for atmospheric loading of NH 4 and NO3 for Choctawhatchee Bay are 0.96 and 7.11 kilograms per hectare per year ( kg
ha - 1 yr -1 ) , respectively.



### Biological Summary

Seagrasses in Choctawhatchee Bay

Seagrasses are important marine foundation species and are highly productive plants (Hughes et al

. 2009)

. Their extensive root systems and dense, structured leaf canopies form hab itat and pr ovide food for a wide array of organisms

, including commercially and recreationally important fish and invertebrates, wading birds, manatees, and sea turtles ( Short and Wyllie

- Echeverria 1996 ; Williams and
Heck 2001 ). Seagrasses enhance sedimen t stability, decrease wave energy , and increase water clarity (see reviews by Phillips and McRoy 1980 ; McRoy and Helfferich 1977)



### .

Adverse impacts to seagrasses come from a variety of sources, including reduced water quality and clarity, overgrazing, and physical damage from boats, dredging

, and development. M onitoring seagrasses has become one of the best methods for determining the overall condition of the nearshore aquatic environment because these plants are sensitive to environmental stressors

. Seagrass
communities have bee n proposed as “coastal canaries ”— biological indicators of changing coastalNutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 9 July 2010 conditions (Orth et al. 2006). Seagrasses have been shown to be adversely impacted by anthropogenic
nutrient enrichment (Orth and Moore 1983 ; Tomasko et al

. 1996).

Reduced underwater light penetration appears to be a primary driver of seagrass decline. The accepted thinking on this process is that increased inputs of nitrogen and phosphorus lead to the excess growth of phytoplankton and epiphytic algae reducing available light to the seagrasses and causing decreased seagrass productivity and ultimately large

- scale seagrass loss es (Duarte 1995)

. This explanation , while valid, does not give a complete picture of the synergistic factors controlling seagrass production. “ Top

down ” food web effects must also be considered. In controlled, in situ experimental studies in St. Joseph Bay, Heck et al

. (2000), found that mesograzers (amphipods, caridean shrimp, gastro pods, and hermit crabs) controlled the effects of nutrient enrichment on the abundance of epiphytes. It is therefore critical to consider the role of “top

- down” effects from overfishing or other food web disruptions in assessments of nutrient enrichment i n estuaries such as Ch octawhatchee Bay.

The seagrass beds in Choctawhatchee Bay are considered extremely important because they support diverse populations of fish and invertebrates, including many recreational and commercial species ( NWFWMD 1996). Seagrass beds in Choctawhatchee Bay contain primarily shoal grass ( Halodule wrightii ) and wigeon grass ( Ruppia maritima ). Shoal grass has flat, narrow leaves and a shallow root
system. It has been characterized as rather tolerant of environmental stresso rs, withstanding heat, desiccation, and turbidity more readily than Thalassia testudinum (turtle grass) or Syringodium filiforme (manatee grass) (USAF 1996 ; Dawes et al. 2004 ). Shoal grass can grow in deeper, lower

- light conditions than other seagrass spe cies and can colonize disturbed areas, preparing sediments for the recruitment
of other species (W olfe 1988). Populations of shoal grass occur mainly in the western portion of the bay. Wigeon grass is found primarily in Hogtown Bayou ( Figure 3) ; it is most common in brackish waters but can tolerate higher salinities (USAF, 1996).

Trends in Seagrass Distribution

Although the seagrass beds in Choctawhatchee Bay are considered crucial habitat , only limited studies
have been conducted in the bay to d etermine the status and tre nds of those seagrass resources. As part of a larger study that covered the entire Gulf of Mexico, McNulty et al

. (1972) reported 3,057 acres of seagrasses in Choctawhatchee Bay. This mapping was done with limited field verific ation, and seagrass species were not identified. The i nterpretation of aerial photographs by Burch (1983) indicated significant loss of seagrass beds for most areas in the bay between 1949 and 1985. Burch also noted that early aerial photography (1949

– 19 80) wa s at various, potentially incompatible scales and did not cover the entire bay at any on e time. Ruth and Handley (2002 ) found that these differences make direct comparisons to current data difficult

.

Further standardized mapping of seagrass beds i n Choctawhatchee Bay, at the appropriate spatial and temporal scales, is needed to determine historical and current trends in various zones of the bay. In

depth monitoring of seagrass health, including acquiring data on species present, coverage, epiphyte loads, associated organisms, N:P ratios, and other parameters, is also needed in the Choctawhatchee Bay system.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 10 July 2010 1992 U.S. Geological Survey National Wetlands Research Center Seagrass Mapping Study (Ruth and Handley, 2002)

The most extensive mapping study of seagrass coverage for the Choctawhatchee Bay area was
conducted in 1992 by the U.S. Geological Survey (USGS) National Wetlands Research Center (NWRC) by using natural

- color aerial photography taken in 1992 at a 1:24,000 scale

, as part of t he northeastern Gulf
of M exico seagrass mapping project. This study differentiated between continuous and patchy seagrass

areas and reported on historical change. For th e study, the bay was divided into three segments , as follows ( Figure 4):

**•** Western Choctawhatchee Bay includes all areas west of the U.S. Highway 293 Mid

Bay Bridge to Brooks Bridge, where Santa Rosa Sound begins. This is the most saline segment of the bay and includes the deepest sections, up to 13 m. It is also historically the area with the most shoreline development , including the cities of Fort Walton Beach, Destin, Niceville

, and Valparaiso , a s well as Eglin A ir Force Base

. This section contains East Pass, the connection to the G ulf of Mexico.

**•** Middle Choctawhatchee Bay, the largest bay segment, covers the area east of the
Mid

- Bay Bridge to the State Road 331 Bridge

. Most of the northern shore consists of the Eglin Air Force Base W ildlife M anagement A rea and contains several creeks and bayous. The southern shoreline contains Horseshoe and Hogtown Bayous and the Sandestin resort. Most of this section of the bay is classified as Class II waters ( shellfish propagation and harvesting ) and contains the majori ty of the bay’s oyster

resources.

**•** Eastern Choctawhatchee Bay includes all areas east of the State Road 331 Bridge
and contains the Choctawhatchee River delta. The Choctawhatchee River is designated as an OFW, and the eastern portion of the bay is classi fied as Class II waters ( shellfish propagation and harvesting ) . Water depths average 3 m in this portion of the bay.

The data show that seagrass beds occur r ed primarily in the western and middle sections of the bay, which are the higher

- salinity areas of the bay (Table 3 and Figure 5 ). The total seagrass coverage for Choctawhatchee Bay was 4,261 acres (Table 3 ). Data indicate that most seagrass areas were patchy beds (3,477 acres), with only 783 acres of continuous beds. Most patchy seagrass coverage , and nearly all continuous coverage, was located in the western

, higher

- salinity segment of the bay.

Because the segments of the bay have very di fferent physical characteristics, it is possible to make only general observations about changes over time. Figures 6 and 7 show the results of a seagrass coverage comparison for Choctawhatchee Bay and Western Choctawhatchee Bay, respectively, in 1992 and 2003.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 11 July 2010 Table 3

. Choctawhatchee Bay seagrass status, 1992 (from Ruth and Handley 2002).

- = Empty cell/no data

Data source: USGS photointerpretation of 1:24,000

- scale natural color aerial photography flown by Stennis Space Center (NASA), fall 1992 Bay Segment Classification Ha Acres

Western Continuous 317 783

- Patchy 1, 109 2,739

Middle Continuous 0.4 1

- Patchy 297 733

Eastern Continuous - -

- Patchy 2 5

Total Continuous 314 784

- Patchy 1,408 3,477

Grand Total - 1,722 4,261 Figure 4. Choctawhatchee Bay segments for seagrass mapping study.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 12 July 2010 Other Factors Affecting Seagrass es

Significant r iverine input and poor flushing heavily influence the hydrodynamics of the bay and may be in part responsible for fluctuations of seagrass coverage. Ruth and Handley (2002) suggest that
historical eutrophication and propeller scarring by boats are in par t responsible for s eagrass loss.

Boats operating in shallow waters, especially waters less than 2 m

, can scar seagrass beds. Th is is occurring in many coastal areas throughout the state, including Choctawhatchee Bay. A 1995 statewide study by the FWRI used aerial photogr aphy to investigate the severity of propell er scarring in seagrass
beds. The i mpacted acreage in Choctawhatchee Bay was approximately 390 acres (approximately 11.3% of the total estimated SAV coverage of 3,450 acres). Approximately 9% was lightly scarred , 2.3% was moderately scarred, and there were no severely scarred areas (Sargent et al. 1995).

FDEP has recognized the need to reduce the scarring of seagrasses by boats and committed resources to
address the issue. Management recommendations include education, channel marking, increased enforcement, and limited motoring zones ( Sargent et al. 1995 ). Additionally, the restoration of scarred
beds may be enhanced by attracting shorebirds to an affected area through the deployment of perching

areas. The nu trient input from the resulting bird guano encourages SAV to grow in the scarred zone (Kenworthy et al. 2000).

FWRI geographic information system ( GIS ) data layers ( 2003 ) indicate that SAV was reduced to an estimated 2, 604 acres in Choctawhatchee Bay

. P reliminary 2009 data from Lazzarino and Terrell (2010), however, indicate 3

, 555.8 total acres of seagrass beds in Choctawhatchee Bay (Table 4) . They are currently conducting a study to quantify seagrass coverage in Choctawhatchee Bay using Landsat 5 TM

im agery and extensive ground

- truthing. Lazzarino and Terrell (2010) suggest that the 2003 mapping
work underestimated the total coverage for the bay because all of the seagrass coverage in the Hogtown Bayou area was missed. This omission was possibly due to a poor visual signature for this

area.

Livingston (2010) suggests that the spatial an d temporal pattern of seagrass loss may be related to changes in the optical characteristics of the water column ( i.e

. , changes in color, turbidity, etc.). Most of
th e losses have been in deeper regions, wh ile SAV coverage has actually increased in shallower areas. Livingston (2010) asserts that t hese patterns of change indicate that reduced light transmission is responsible for the observed response.

Table 4. Choctawhatchee Bay t otal seagrass coverage estimates , in acres.

*Estimate missed all seagrass coverage in Hogtown Bayou area

. **Data are preliminary but include extensive groundtruthing.
1992 (USGS) (Ruth and Handley 2002) 2003 (FWRI)* 2009 ( Lazzarino and Terrell)**

4,261 2,064 3,556Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 13 July 2010 Figure 5. Seagrass coverage in Choctawhatchee Bay, 1992.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 14 July 2010 Figure 6

. Choctawhatchee Bay seagrass coverage comparison, 1992 and 2003 (Alexander 2010).

Figure 7 . Western Choctawhatchee Bay seagrass coverage comparison, 1992 and 2003 ( Alexander 2010)

.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 15 July 2010 Tidal Marshes in Choctawhatchee Bay The fringing (emergent) vegetation zones in t he Choctawhatchee Bay system are not well developed

, and the area of marsh habitat is lower than that found in other estuaries in the region. Emergent

v egetation is limited to a few peripheral areas bordering bayous, Live Oak Point, and the marshes
around the river delta (Livingston 2010)

. In 1972, emergent marsh coverage was es timated to be 2,816 acres (NOAA 1991). Livingston (1986) calculated that 1,855 acres of m a rsh were present in 1976 , based

on USGS topographic maps, and NOAA (1991) calculated that 2,700 acres of marsh were present in

1985

, based on a erial photographs. A 1988 NOAA survey of the areal extent of coastal wetlands in Gulf of Mexico estuaries found that Choctawhatchee Bay ha d 2,700 acres of salt marsh, and 3,700 acres of freshwater marsh (Reyer et al. 1988). An FDEP estimate of emergent marsh based on FWRI GIS data layers (1994

– 2006) was 2, 411 acres

.

The discrepan cies among estimates illustrate the difficulty of comparing the results from different imagery and methods of calculating area. Livingston (1986) found the dominant species to be the salt

tolerant perennial Juncus roemerianus , with significant coverage by Spartina alterniflora

. A complete vegetation survey of marshes in Choctawhatchee Bay has not been conducted, but Keppner and Keppner (2003), surveyed the Hogtown Bayou area ( including the smaller bayous Mussett Bayou,

Hewett Bayou, and Mack Bayou) ( Figure 8 ). Keppner and Keppner (2003) found a total of 61 species of vascular plants in fresh, brackish

, and salt marshes (Table 4) . The fresh marshes contained 42 plant species, while the brackish and salt marshes contai ned 5 an d 14 species , respectively. Livingston (1986)
and others note that there is historic al anecdotal evidence for the loss of marshes in Choctawhatchee Bay following the opening of East Pass and the shift from a primarily fresh system to a more saline,

strati fied system.

Table 4. Vascular plants from Hogtown Bayou tidal marshes ( from Keppner and Keppner 2003).

- = Empty cell/no data Family Genus and Species

Salt marsh

- Aquifoliaceae Ilex vomitoria

Asteraceae Baccharis halimifolia

Asteraceae Iva frutescens

Convolvulaceae Ipomea sagittata

Cyperaceae Eleocharis robinsii
Cyperaceae Scirpus robustus

Gentianaceae Sabatia stellaris

Juncaceae Juncus roemerianus

Malvaceae Kosteletzkya virginica Plumbaginaceae Limonium carlinianum

Poaceae Distichlis spicata

Poaceae Paspalum vaginatum

Poaceae Spartina patens Asclepiadaceae Cyananchum angustifolium

Brackish marsh

-

Asteraceae Baccharis angustifolia
Cyperaceae Cladium jamaicense
Cyperaceae Fuirena breviseta
Cyperaceae Scirpus etuberculatus

Fabaceae Sesbania puniceaNutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 16 July 2010 Family Genus and Species

Freshwater marsh - Apiaceae Hydrocotyle bonariensis

Asteraceae Aster chapmanii

Asteraceae Bigelowia nudata

Asteraceae Coreopsis linifolia

Asteraceae Helianthus angustifolium

Asteraceae Eupatorium mohrii

Clusiaceae Hypericum hypericoides

Clusiaceae Hypericum mutilum
Cyperaceae Carex festucacea
Cyperaceae Cyperus polystachyos
Cyperaceae Dichromena colorata
Cyperaceae Dichromena latifolia
Cyperaceae Fimbrystylis autumnalis
Cyperaceae Psilocarya nitens
Cyperaceae Rhynchospora cephalantha
Cyperaceae Rhynchospora ciliaris
Cyperaceae Rhynchospora fascicularis
Cyperaceae Rhynchospora wrightiana
Cyperaceae Scleria reticularis

Droseraceae Drosera capillaris

Eriocaulaceae Eriocaulon decangulare

Haemodoraceae Lophiola americana

Juncaceae Juncus abortivus

Juncaceae Juncus acuminatus

Juncaceae Juncus marginatus

Lentibulariaceae Utricularia biflora

Lentibulariaceae Utricularia cornuta

Liliaceae Aletris lutea
Onagraceae Ludwigia decurrens
Onagraceae Ludwigia linearis
Onagraceae Ludwigia linifolia
Onagraceae Ludwigia pilosa

Poaceae Dicanthelium scabriusculum

Poaceae Echinochloa colona

Poaceae Erianthus strictus

Poaceae Manisuris rugosa

Poaceae Panicum verrucosum Scrophulariaceae Agalinis linifolia Scrophulariaceae Bacopa monnieri Xyridaceae Xyris baldwinii Xyridaceae Xyris fimbriata Xyridaceae Xyris jupicai Total number of species 61Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 17 July 2010 Figure 8

. Location of Hogtown Bayou study area for vascular plant inventory and invertebrat e sampling (Keppner and Keppner 2003).

Phytoplankton

In Choctawhatchee Bay, Blaylock (1983) observed peaks in phytoplankton production correlated with freshwater inflow, w hich in turn was associated with increase s in nutrient concentrations. Chlorophyll

p eaks occurred during a period of high rainfall in April and following a hurricane in September 1975.

Livingston conducted m onthly biological sampling of Choctawhatchee B ay from 1985 to 1998 (Livingston

2010 )

, including phytoplankton sampling and taxonomic analysis. Figure 9 shows t he location s of the fixed sampling stations. In addition, a 2006 study examined phytoplankton assemblages in several bayous in the Choctawhatchee Bay system (Livingston 2010)

.

P hytoplankton cell numbers ( Figure 10 ) were lowest at the river mouth and highest at S tat ions C38 and C36e. Species richness was lowest in the eastern parts of the bay, and increased in the western

sections

, with peaks at S tations C38 and C36e. From 1985 to 19 86, the dominant species collected were
Chaetoceros spp., Coscinodiscus spp., Skele tonema costatum

, Pyrocystis sp ., Chaetoceros coarctatus

, Cyclotella sp., and Ceratium tripos

. Blooms ( Skeletonema costatum, Falcula hyalina ) were found mainly in Old Pass Lagoon (C36e) ( Figure 11). The highe st annual average phytoplankton numbers were no ted in Old Pass Lagoon and extre m e western sections of the bay, with annual averages greater than otherNutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 18 July 2010 stations in the bay. In contrast to Blaylock (1983), Livingston (1986) reported peak phytoplankton numbers during December; low numbers occurred in spring and summer months, which are periods of high predation by herbivorous organisms ( i.e

., zooplankton, meroplankton) (Livingston 2010).

In April 2006, water samples were taken at stations throughout Choctawhatchee Bay, including several bayous, and preserved and analyzed by Dr. A.K.S.K. Prasad, at Florida State University (FSU)

. Phytoplankton species identifications and cell counts were conducted. No blooms were present, except for the Chula Vista Bayou surface sample, where bloom concentrations ( > 10 6 cells L -1 ) of Chaetoceros affinis were observed. A potentially harmful diatom, Pseudonitzschia ( possibly pseudodelicatissima) sp.

, was present in almost all of the stations examined but not in bloom densities. According to the Manual of Harmful Mar ine Microalgae (Hallegraeff et al. 2003), Pseudonitzschia may produce domoic acid, a
toxin that causes amnesic shellfish poisoning (ASP). It is important to note, however, that domoic acid was not present in these samples. Cyclotella choctawhatcheeana an d Chaetoceros laevis were also
present. The overall assemblages in all of the stations were similar. The dinoflagellates Prorocentrum
triestinum

. P. micans

, and P. cordatum (syn. P. minimum ) were present in very low numbers. All three species are known to form red tide blooms. Karenia brevis was not observed. No harmful raphidophytes were encountered. For a detailed description of phytoplankton analytical methods and
the results for each station, see Livingston (2010).

Invertebrates

Livingston sampled infauna and benthic macroinvertebrates as part of a biological sampling program in Choctawhatchee Bay (Livingston 2010). Infaunal samples were taken monthly with coring devices at the fixed stations in Choctawhatchee Bay from 1985 to 1998 ( Figure 9) . Epibenthic invertebrates and fishes

were collected monthly for the same period and stations, with 5 m otter trawls . Species were identified, biomass was calculated, and all biological da ta were transformed to trophic units. Infaunal numbers were generally lower at 2 stations in the upper parts of the western bay and at the mid

- bay (deeper)

stations. Peak numbers were in western sections of the bay near East Pass.

The overall numbers o f trophic units were lowest at the mouth of the Choctawhatchee River and at the
mid

- bay stations. The distribution of FII (infauna, epibenthic invertebrates, and fish) biomass followed this pattern , while the FII species richness was lower at the mid

- bay stations

, with increases in the western parts of the bay. The bay infauna were particularly reduced in deeper parts of the bay. Figure 12 presents an a nalysis of fish and infaunal numbers in bayou areas

. The highest numbers of infauna were found in eastern bayous , areas that were not adversely affected by urban development. Infaunal numbers were lowest in lower Rocky Bayou and Boggy Bayou (Stations 28 and 29). Fish numbers were highest in the eastern bayous

, with marke d reductions in Hogtown Bayou (S tation 17), Garnier Bayou

, and Old Pass Lagoon. Overall, the numbers of infauna and fishes were lowest in areas receiving
stormwater runoff from urban areas.

Foster (2000) provided an extensive systematic list of invertebrates for Choctawhatchee Bay that contains 209 species in 175 genera in 7 phyla

. F or the complete tax a list, see Keppner and Keppner ( 2003). Heard et al. (2000

, 2002) reported on the benthic invertebrate community of Choctawhatchee Bay in relation to Gulf sturgeon forag ing. Fox et al

. (2001) provided a list of macroinvertebrate species related to sturgeon locations. Table 5 contains a summary list of the taxa reported by Foster (2000) and

Fox et al. (2001) for Choctawhatchee Bay

. These studies do not compare invertebr ate taxa richness or abundance in Choctawhatchee Bay to other regional estuaries.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 19 July 2010 Table 5. Benthic macroinvertebrates reported from Choctawhatchee Bay ( after Foster 2000
and Fox et al. 2001)

. Phylum Number of

Genera Number of Species

Cnidaria 3 3 Platyhelminthes 1 1

Nemertea Not stated 3

Annelida 71 83

Mollusca 36 47 Arthropoda 60 68

Echinodermata 4 4

Total 175 209

Figure 9. Location of Choctawhatchee Bay biological sampling stations, 1985

– 98 (Livingston 2010).Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 20 July 2010 Figure 10. Phytoplankton cell numbers and species richness at mid

- bay stations in Choctawhatchee Bay and East Pass Lagoon ( S tation 36e)

, averaged from monthly data, September 1985

– August 1995 (Livingston 2010). Phytoplankton

0 5000000 10000000 15000000 20000000 25000000 30000000003D007D011D015D019D022D025D031D034D038D36ED

station 0 5 10 15 20 25 30 35 40# taxa TOTALN NBRTAXANutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 21 July 2010 Figure 11. Phytoplankton bloom numbers at mid

- bay stations in Choctawhatchee Bay and East Pass Lagoon (S tation 36e)

, averaged from monthly data

, September 1985

– August 1995 (Livingston 2010)

. Phytoplankon blooms

1 1000 1000000 1000000000003D007D011D015D019D022D025D031D034D038D36ED

station Skeletonema costatum Chaetoceros socialis Falcula hyalinaNutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 22 July 2010 Figure 12. Total numbers of infauna and fish, averaged from monthly data from September 1985

– August 1995 (Livi ngston 2010 ).

Fisheries in Choctawhatchee Bay

Commercial and sport fisheries are important in the area, as is oyster harvesting (Ruth and Handley

2002 ). Commercially and recreationally important fish and shellfish include shrimp ( Penaeus spp.),

eastern oysters ( Crassostrea virginica ), spotted seatrout ( Cynoscion nebulosus ), gulf menhaden ( Brevoortia patronus ), red drum or redfish ( Sciaenops ocellatus ), blue crab ( Callinectes sapidus ), G ulf flounder ( Paralichthys albigutta ), striped mullet ( Mugil cephalu s ), and white mullet ( Mugil curema ).

T he Choctawhatchee B ay system supports the gulf sturgeon ( Acipenser oxyrinchus ), a federally
threatened species, which migrates through the bay into the Choctawhatchee River to spawn. In the
Choctawhatchee River and B ay system , juvenile (age 1 to 6 years ) Gulf sturgeon migrate and use habitat differently than they do in other regional systems. Instead of remaining near the river mouth for the entire year, they use Choctawhatchee Bay in the winter, returning upriver to resting areas in the spring (USFWS 2003). A study of sub

- adult (age 4 to 7 years ) G ulf sturgeon in Choctawhatchee Bay found that 78% of tagged fish remained in the bay the entire winter, with the res t in connect ed waters and the Gulf
of Mexi co (USFWS 2003). These findings illustrate the importance of Choctawhatchee Bay as a wintering area to this protected species.

The Choctawhatchee Basin is home to the Okaloosa darter ( Etheostoma okaloosae ), ano ther federally endangered species. This small fish is known only from the main channels and small tributaries of 6 clear stream systems that drain into Rocky and Boggy Bayous of Choctawhatchee Bay. Over 98% of the

range of the Okaloosa darter is within t he Eglin Air Force Base Wildlife Management Area, afford ing the species considerable protection from development and habitat disturbance. Populations have been Bayou infaunal and fish numbers

0 20 40 60 80 100 120 140005D009D013D017D027D028D029D040D041D36ED

station 0 200 400 600 800 1000 1200 1400fish numbers TOTATinfN TOTALfishNNutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 23 July 2010 stable or increasing in the past 15 years, and significant habitat restoration has taken place. These developments have led to a recent proposal to change the status of the Okaloosa darter from endangered to threatened (USFWS 2010).

Marine Fisheries Independent Monitoring

The FMRI (currently FWRI) Marine Fisheries Independent Monitoring Program conducted fixed station sampling of fishes and invertebrates in Choctawhatchee Bay from 199 3 to 199 5. This sampling was part of a larger sampling effort that also included stratified random sampling in the Choctawhatchee Bay/Santa Rosa Sound system (1993

– 96)

. The 8 f ixed station locations were based on representative bay habitat types. Collections were made monthly with three gear types: beach seine, offshore seine,
and trawl. In 1996, only stratified random sampling was conducted, also with three gear types: beach seine, offshore seine, and trawl. These data provide valuable information on the life history, growth,
and recruitment for each species collected. These data also provide general information on the ecological condition of the bay. Data fro m th e program have been used to develop stock assessments for blue crab, red drum, mullet

, and spotted sea trout. Preliminary recruitment indices have been developed for many of these species and can be tested against adult landings when the fish are larg e enough to enter the fishery (FMRI, 1993

– 96)

. Tables 6 through 9 show c atch s tatistics for n umerically
d ominant t axa from fixed station sampling in Choctawhatchee Bay from 1993 to 1996 (FMRI, 1993

– 96)

.

Table 6

. In 1993 , a total of 513,517 organisms, representing 108 taxa

, were collected. Species Number % Lagodon rhomboides 318,090 61.9 Brevoortia spp. 73,082 14.2

Leiostomus xanthurus 72,103 14.0 Menidia spp. 16,863 3.3
Penaeus spp. 5,285 1.0 Orthopristis chrysoptera 4,745 .92 Eucinostomus spp. 2,659 .52

Membras martinica 2,664 .52 Mugil spp. 2,475 .48 Anchoa spp. 2,332 .45 Micropogonias undulatus 2,191 .42 Callinectes sapidus 1,897 .37

Gobiosoma robustum 1,841 .36

Bairdiella chrysoura 1,310 .26 Syngnathus scovelli 534 .1 Sciaenops ocellatus 511 .09

Subtotal 508,582 99.03

Total 513,517 100Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 24 July 2010 Table 7. 1994 Fixed

- station sampling yielded 459,835 organisms representing 117 taxa. Species Number % Anchoa spp. 249,024 54.2

Leiostomus xanthurus 123,471 26.9 Lagodon rhomboides 37,309 8.1 Menidia spp. 11,390 2.5

Mugil spp. 10,963 2.4 Eucinostomus spp. 9,623 2.1

Brevoortia spp. 6,056 1.3

Penaeus spp. 1,751 .4 Callinectes sapidus 1,675 .4 Orthopristis chrysoptera 1,141 .25

Bairdiella chrysoura 768 .17

Prionotus scitulus 680 .15 Cynoscion arenarius 618 .13

Gobiosoma robustum 542 .12

Subtotal 455,011 98.95

Total 459,835 100

Table 8

. 1995 fixed

- station sampling yielded 470,763 organisms representing 105 taxa. Species Number %

Leiostomus xanthurus 324,330 68.9 Lagodon rhomboides 74,101 15.7 Mugil spp. 24,274 5.2 Menidia spp. 13,787 2.9 Brevoortia spp. 8,647 1.8

Anchoa spp. 4,333 .9 Micropogonias undulatus 3,606 .8
Penaeus spp. 3,361 .7

Eucinostomus spp. 3,169 .7 Orthopristis chrysoptera 1,254 .3 Callinectes sapidus 1,166 .2 Bairdiella chrysoura 771 .2

Gobionellus boleosoma 650 .1 Clupeidae spp. 530 .1

Subtotal 463,979 98.5

Total 470,763 100Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 25 July 2010 Table 9

. 1996 stratified random sampling by seine and trawl yielded 462,945 organisms representing 711 taxa.

Beach and offshore seine sampling results

Species Number %

Leiostomus xanthurus 68,674 34.4 Menidia spp. 53,703 26.9 Lagodon rhomboides 18,696 9.4 Mugil cephalus 12,483 6.2 Harengula jaguana 11,726 5.9

Anchoa mitchilli 8,911 4.5 Eucinostomus spp. 5,580 2.8

Brevoortia spp. 4,912 2.5 Anchoa lyolepis 2,584 1.3 Anchoa hepsetus 1,695 0.8

Subtotal 188,964 94.7

Total 199,900 100

Trawl sampling results

Species Number %

Leiostomus xanthurus 231,233 87.9 Micropogonias undulatus 7,185 2.7

Anchoa mitchilli 6,208 2.4 Brevoortia spp. 5,943 2.3 Lagodon rhomboides 6,050 2.3

Penaeus duorarum 730 0.3 Callinectes sapidus 664 0.3 Penaeus spp. (<15 mm pohl) 459 0.2 Bairdiella chrysoura 378 0.1 Anchoa lyolepis 375 0.1

Subtotal 259,225 98.6

Total 263,045 100

Shellfish Harvesting

The Shellfish Environmental A ssessment Section (SEAS) of the F lorida Department of Agriculture and Consumer Services (FDACs) regulates shellfish harvesting in the s tate

. SEAS conducts comprehensive surveys of shellfish harvesting areas to ensure that shellfish are grown and harvested in a safe and sanitary manner. For the purposes of regulating shellfish harvesting in Florida, “shellfish” are defined as
edible taxa of oysters, clams, and mussels. These filter

- feeding mollusks filter up to 400 gallons of water per day, retaining much of the dissolved and suspended m aterial, including microorganisms and
chemical contaminants.

The primary species of shellfish harvested in Choctawhatchee Bay is the eastern oyster ( Crassostrea virginica ). The northern hard

- shell clam or quahog ( Mercenaria spp.) and the brackish water or marsh clam ( Rangia cuneata ) are also found in Choctawhatchee Bay but not in commercial quantities. Choctawhatchee Bay represents less than one

- tenth of 1% of commercial shellfish landings and value in
Florida. Harvesting areas are categorized based on their fecal coliform levels, and any pollution sourcesNutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 26 July 2010 that may be in the vicinity. Choctawhatchee Bay shellfish harvesting area s (contained in the “Middle”
and “Eastern” area s of the bay) are classified as “condi tionally approved” and “prohibited ” ( Knight and
Wallman 2007 ).

Oyster harvesting seasons in Choctawhatchee Bay are currently January 1 to June 30, and October 1 to
December 31.

Red Tide and Associated Animal Mortality Events

A red tide event and associa ted bottlenose dolphin mortalities were reported for Choctawhat chee Bay and nearshore Gulf waters from August 1999 to January 2000 (Livingston 2002). Over 100 dolphins died, and researchers found brevetoxins (the Karenia brevis toxin) in the animals’ syst ems.

A red tide event was present in the Florida Panhandle from August to December 200 5, following the northwest transport of a red tide event initiated in the eastern Gulf of Mexico

. The FWRI investigated aquatic animal mortalities in Choctawhatchee Bay during and following this red tide event

. Garnier Bayou was the most adversely affected area of the bay. Dead species reported included Gulf sturgeon ( Acipenser oxyrinchus desotoi ), bay anchovies ( Anchoa mitchilli ), skipjack shad ( Alosa chrysochloris ), and juvenile spot ( Leiostomus xanthurus ). NOAA, with assistance from FWRI, investigated associated bottlenose dolphin mortalities. High concentrations of brevetoxins were found in the internal organs of fish (sturgeon, gar, and mult iple juvenile fishes ) , and indications were that the toxin exposure was postbloom (FWRI website)

. High levels of brevetoxin were detected in several food web components,
and brevetoxin is considered the primary cause of the fish kills and marine mammal mortaliti es. The findings also suggest that brevetoxin may persist in estuarine and coastal waters, and circulate through
the food web after a Karenia brevis bloom has ended. Animals c an be exposed to lethal doses of brevetoxin weeks to months after a bloom has dissipated (FWRI website)

.

No other harmful algal bloom ( HAB ) species or toxins have been identified in connection with the Choctawhatchee Bay aquatic animal mortalities. Alth ough background levels of a potentially toxic
diatom ( Pseudonitzschia sp.) were detected in some samples, no domoic acid (the toxin produced by the diatom) was present in any biological or water samples tested. As part of the Choctawhatchee Bay mortality investigation, FDEP provided data on contaminant sampling from Garnier Bayou. The results
indicate that no other contaminant s were involved in the ongoing fish kill (FWRI website). FWRI staff
have indicated that red tide ( Karenia brevis) outbreaks are an offshore phenomenon, but may migrate
toward shore. K. brevis , however, is a marine species and does not survive in lower salinity (<20 ppt) environments, such as nearshore or estuarine waters. Based on these factors, FWRI staff maintain that the effects of added nutrient loads coming from man’s activities on the land and delivered to estuaries and coastal waters are not responsible for initiating the offshore blooms or exacerbating blooms in
Florida’s waters. Prel iminary studies by FWRI scientists indicate that the major nutrient source for K.
brevis is from species mortality, linked with a red tide event. Therefore, based on current information, waters will not be placed on Florida’s list of impaired waters based on the outbreak of red tide. In summary, when it is determined that a specific, reoccurring HAB adversely affects the designated use of a particular waterbody and is caused by pollutant, that waterbody will be added to FDEP’s verified list of impaired wate rs.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 27 July 2010 

### Water Quality Studies

CBA Partnership with University of Florida LakeWatch/Project COAST Program

The CBA formed a partnership with the University of Florida (UF) LakeWatch / Project COAST P rogram in

199 6 to begin the coordination of water quality monitoring in Choctawhatchee Bay

. This effort was
initiated to document spatial variability and long

- term changes in the bay’s water quality

. As part of t he

program , 90 s tations are sampled monthly for TN, TP, chlorophyll a , and water clarity (Secchi dep th),
and the s amples are sent to the U F LakeWatch program for analysis. For each station, DO , pH, turbidity, temperature, and salinity are measured at the surface and bottom

. The CBA also collects quarterly color readings.

FDEP notes the following deta il s about sample analysis methods that may require additional scrutiny before using the results of the data to inform water quality standards development :

1. Chlorophyll a is reported without correction for phaeophytin. F DEP has determined that phaeophyton

- corrected chlorophyll a are more appropriate for water quality

criteria

, and therefore the uncorrected (less accurate) chlorophyll a data may be
considered as estimated values

.

2. The method for the determination of TN in water samples is not an EPA

- approved method, nor is it an approved method in the F DEP Standard Operating Procedures (SOPs). Bachmann and Canfield (1996) describe this method and provide data that show the method produces results comparable to EPA

- approved methods for TN in fresh water. Water samples are frozen before analysis, another method that also does not conform to F DEP SOPs. However, Bachmann and Canfield (1996) and Canfield et al. (2002) demonstrate that TN results are not significantly affected by freezing. Project COAST samples are held froze n for a maximum of 3 months before analysis.

3. TP samples are also frozen, rather than acidified, before analysis. Canfield et al. (2002) showed that this preserva tion method did not significantly affect the analytical results.

Due to the inconsistencies between Project COAST lab analyses and F DEP SOPs and EPA requirements

, FDEP conducted several analyses in which the water chemistry results from Project COAST we re compared with results from concurrent sampling by other entities that used National Environmental Laboratory Accreditation Conference ( NELAC )- certified labs and approved methods. The results of these analyse s suggest that it is appropriate to use the l ong

- term Project COAST datasets, in conjunction with other data sources, where available, to inform numeric nutrient criteria proposals.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 28 July 2010 C

BA/Okaloosa

- Walton College Long

- Term Sampling and Data Coordination
Study Area

Choctawhatchee Bay is located in the Panhandle region of northwest Florida (Figure 13 ). The main tributary to the bay is the Choctawhatchee River at the eastern end of the bay , while East Pass, located near the west end of the bay, is the only direct outlet to the Gulf of Mexico. The bay is approximately 29.2 miles from east to west and about 3 miles wide at its widest point. Choctawhatchee Bay has a surface area of 86,295 acres and is the third largest estuarine system on the Gulf coast of Florida (McNu lty et al. 1972). T he bay has a maximum depth of 43 feet just north of the East Pass. Two channels, Santa Rosa Sound to the west and the Intracoastal Waterway to the east

, connect Choctawhatchee Bay to Pensacola Bay, and to West Bay in Panama City, respe ctively (Blaylock 1983).

Figure 13

. Choctawhatchee Bay is located in the Panhandle region of Florida

, within Okaloosa and Walton Counties ( top ). C urrently , the C BA samples almost 90 stations sampled monthly throughout Choctawhatchee Bay ( bottom ). Each red dot is a sampling station.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 29 July 2010 Project Scope

Walton and Okaloosa Counties are like any other c oastal Floridian c ounty

, in that they are experiencing record high population growth rates

, and the expected population growth rates for each county are

st aggering. A comprehensive evaluation of the current and historical water quality is needed. The

w ater quality of the estuary system is evaluated first spatially along the horizontal stretch of the bay and then temporally over the 40 years of data record.

Data Summary

The C BA of Okaloosa

- Walton College in Niceville, Florida, has been coordinating monthly water sampling
within the Choctawhatchee Basin for over 10 years. All available water chemistry data (EPA data collected in 1968, University of West Florida [ UWF] data collected in 1975, CAMA data collected in

1985

– 87, and CBA/L akeWatch data collected from 1991 to 2007) have been joined into one dataset and assigned to 1 of 6 sections based on their location ( Section 1 is located near the river

, and Secti on 6 is
located near East Pass ). Different researchers have collected data over a time sp an of 40 years.

D ifferent field sampling techniques, laboratory methods, and station locations were used throughout all
studies.

Spatial differences in water quality were evaluated by calculating averages for each of the six sections.

T- tests were performed on the means to determine if the means were statistically different from each
other. Temporal differences in water quality were determined by following t he methods described by
Terrell et al. (2000).

Table 1 0 summarizes w ater chemistry data over the 40 years of data collection

. Average TP

, TN

, chlorophyll, color, and turbidity were highest in Section 1 (nearest the Choctawhatchee River) and gradually decreased moving west to Section 6. Secchi depth was typically lowest in Section 1 and increased traveling west to Section 6.

Table 11 temporally summarizes water quality parameters over the 40 years of record within each

section

. Seasonal differences exist in the sections of the bay closest to the river but not in sections of the bay closer to East Pass

. Table 12 summarizes water quality data for 2000 to 2009, collected by the

CBA , for 3 regions delineated by surface salinity.

Conclusions

The importance of long

- term, routine sampling is critical for the preservation of overall good water quality in Choctawhatchee Bay. Groups such as the CBA are providing a valuable, cost

- efficient service to water resource managers throughout the state by coordinating a long

- term, routine sampling program, providing outreach and education to the local community and municipal staffs on how to be good environm ental stewards with the water resources, and executing localized restoration projects to help correct specific problems identified through monitoring.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 30 July 2010 Table 10

. Summary of the spatial water chemistry analyses from six sections along the horizontal length of the Choctawhatchee Bay. Section 1 is located along the east side of the bay near the Choctawhatchee River. Section 6 is located along the west side of the ba y near East Pass. Small letters next to each mean represent statistica lly significant differences ( Terrell 2010 ).

- = Empty cell/no data

Section (sig) - 1(a) 2(b) 3(c) 4(d) 5(e) 6(f)

Period of

Record - 1968

– 2007 1968

– 007 1968

– 2007 1968

– 2007 1968

– 2007 1968

– 2007

TP (mg/L) N 208 139 208 155 142 179

- Mean 0.027(a) 0.018(bcdf) 0.016(bcdf) 0.016(bcdf) 0.012(e) 0.016(bcdf)

- Range 0.000 - 0.170 0.001

- 0,085 0.000

- 0.120 0.000

- 0.160 0.001

- 0.052 0.000

- 0.063

TN (mg/L) N 210 138 210 157 144 181

- Mean 0.456(a) 0.302(b) 0.239(cdef) 0.226(cdef) 0.223(cdef) 0.233(cdef)

- Range 0.000

- 3.070 0.105

- 0.600 0.000

- 0.503 0.000

- 1.000 0.105

- 0.800 0.000

- 1.513

Chlorophyll (μg/L) N 169 118 186 135 124 158

- Mean 6(ab) 6(ab) 3(cdef) 3(cdef) 4(cdef) 3(cdef)

- Range 0- 66 1- 19 0- 23 0- 19 1- 70 0- 17 Secchi depth (m) N 195 136 205 114 100 129

- Mean 1.07(a) 1.53(b) 2.14(c) 2.44d(f) 3.37(e) 2.63(df)

- Range 0.10

- 2.7 0.36

- 4.27 0.65

- 5.79 0.00

- 6.17 1.07

- 7.92 0.83

- 7.00 Color (PCU) N 148 79 158 116 55 128

- Mean 46(a) 30(b) 19(cdef) 17(cdef) 12(cdef) 15(cdef)

- Range 5- 250 3- 115 3- 95 0- 71 3- 50 0- 61 Turbidity

(NTU) N 266 545 571 351 318 361

- Mean 8(abe) 6(abce) 4(bcef) 5(abcef) 3(bcef) 3(cef)

- Range 0- 301 0- 250 0- 214 0- 828 0- 158 0- 105Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 31 July 2010 Table 1 1

. Temporal water chemistry analyses over a 40 -y ea r period of record

, 1968

–

2007 ( Terrell 2010 ).

Parameter Section Seasonality Prob>F Temporal Significance

TP 1 3° 0.9878 No significant change

TN 1 None 0.0148 Significant decrease Chlorophyll 1 6° 0.0405 Significant i ncrease
Secchi depth 1 3° 0.5333 No significant change

TP 2 2° 0.239 No significant change

TN 2 2° 0.0576 No significant change Chlorophyll 2 6° 0.0421 Significant increase Secchi depth 2 4° 0.3213 No significant change

TP 3 None 0.9608 No significant change

TN 3 2° 0.1045 No significant change Chlorophyll 3 None 0.899 No significant change Secchi depth 3 None <.0001 Significant increase

TP 4 None 0.9403 No significant change

TN 4 None 0.0208 Significant increase Chlorophyll 4 None 0.7825 No significant change Secchi depth 4 None <.001 Significant increase

TP 5 None 0.0012 Significant decrease

TN 5 None 0.7782 No significant change Chlorophyll 5 None 0.1095 No significant change Secchi depth 5 None 0.038 Significant increase

TP 6 None 0.0426 Significant decrease

TN 6 None 0.4069 No significant change Chlorophyll 6 None 0.8094 No significant change Secchi depth 6 None 0.6415 No significant change

Table 12. Summary of the spatial water chemistry analyses for three sections (based on surface salinity) along the horizontal length of Choctawhatchee Bay, 2000

– 09. Small letters next to each mean represents statistically significant differences (Lazzarino and Terrell 2010)

. NTU = Nephelometric Turbidity Unit Mean (STD) (statistical significance) Western (a) Middle (b) Eastern (c)

Number of samples 1,074 2,586 995
TP (μg/L) 12 (6) (a) 16 (8) (b) 25 (12) (c)

TN (μg/L) 246 (89) (a) 269 (100) (b) 413 (126) (c)

Chlorophyll a (μg/L) 4 (4) (a) 5 (4) (b) 9 (13) (c)

Secchi depth (m) 3 (1) (a) 2 (1) (b) 1 (0) (c)

Color (PCU) 9 (6) (a) 16 (17) (b) 22 (19) (c)

Bottom depth (m) 0.5

- 11.3 0.34

- 11.0 0.30

- 4.88

Surface salinity (ppt) 22 (6) (a) 18 (8) (b) 11 (9) (c)

Bottom salinity (ppt) 27 (6) (a) 25 (8) (b) 17 (8) (c)

Surface turbidity (NTU) 4 (18) (a) 11 (64) (b) 13 (37) (c)

Bottom turbidity (NTU) 6 (21) (a) 16 (69) (b) 18 (41) (c)Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 32 July 2010 FDEP Water Quality Analyses

FDEP analyzed all of the data available for Cho c tawhatchee Bay from the IWR database

. The period of
record was February 1996 to December 2009, and the spatial scale covered the entire bay system (all segments with waterbody identification numbers [ WBIDs ] characterized as “estuary”). For the IWR
da ta, annual geometric means for the entire bay were calculated for TP, TN, and chlorophyll a

.

Table 12 shows the r esults of these calculations

. Figure s 14 through 16 show trends over the 14

- year period and the long

- term geometric means for each parameter. TP, after an initial increase from 1996

to 19 98, decreas ed from 1998 t o 2002, and was relatively steady from 2002 to 2009. TN concentrations

were relatively steady over the 14

- year period, until a spike in 2008. This spi ke appears attributabl e to localized increases at Chula Vista Bayou over a 3- month period, and the event is still being investigated. Chlorophyll a concentrations were relatively low and steady, with annual geometric means ranging from

2.7 to 3.4 ug/L and a long

- term geometric mean of 2.95 ug/L

. It is important to note that a large percentage (approximately 75%) of the chlorophyll a data were reported as below the minimum detect limit (mdl) of 5 μg/L. Values reported as “below detect” were assigned a value equal to one

- half o f the mdl (2.5 μg/L).

Figures 14 through 16 show the distributions of the baywide geometric means. For all stations poole d,
the long

- term mean annual geometric mean was calculated, and a log normal distribution function was
fit ted to estimate the long

- term 75 th and 90 th percentile of the data (Table 13 ).

FDEP also grouped stations into the three regions used by th e C BA

. These regions are based on salinity,
with mean annual surface salinities of 22 ppt (West), 18 ppt (Middle)

, an d 11 ppt (East). The y roughly correspond to USGS regions based on physical landmarks: west of the Mid

- Bay Bridge, between the
Mid

- Bay Bridge and U.S. H ighway 331 Bridge, and east of the U.S. Highway 331 Bridge (Terrell 2010). Figures 17 through 19 compa re t he distr ibutions of the geometric means for TP, TN, and chlorophyll a for each region

.

Table 1 3

. Summary of data analysis for Choctawhatchee Bay, all stations combined

, 1996

–

2009.

- = Empty cell/no data

LN = N atural logarithm

GM = G eometric mean

C.I. = C onfidence interval. * Long

- term GMs and the 90 th percentile of annual GMs are highlighted.
Choctawhatchee Bay Data TP ( μg/L ) Log Normal
Distibution TP ( μg/L ) Empirical
Percentile TN ( μg/L ) Log Normal
Distibution TN ( μg/L ) Empirical
Percentile Chlorophyll a ( μg/L ) Log Normal
Distibution Ch lorophyll a ( μg/L ) Empirical
Percentile

Mean LN TP 3.029 - 6.013 - 1.083 - S tandard deviation

LN TP 0.438 - 0.207 - 0.090 -

N 2, 027 - 1, 120 - 1, 820 - 95% C.I. 0.02 - 0.01 - 0.00 - Long

- term GM 20.67* 22.70 * 408.58* 416.92* 2.95* 2.96*

Lower 95% C.I. 20.28 - 403.64 - 2.95 - Upper 95% C.I. 21.07 - 413.58 - 2.95 - 75 th p ercentile 27.78 26.26 469.94 450.79 3.14 3.18

90 th p ercentile 36.25 * 39.27* 533.02* 525.99* 3.31* 3.21*Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 33 July 2010 Figure 14

. Trend of annual geometric means for TP in Choctawhatchee Bay, 1996

– 2009 , and long

- term geometric mean.

Figure 15

. Trend of annual geometric means for TN in Choctawhatchee Bay, from IWR dataset

, 1996

–

2009 , and long

- term geometric mean. 0 5 10 15 20 25 30 35 40 45 50

1995 2000 2005 2010 

## Annual Geometric Means TP Choctawhatchee Bay

annual geometric

mean TP

long term geometric

mean TP

0 100 200 300 400 500 600 700

1995 2000 2005 2010 

## Annual Geometric Means TN Choctawhatchee Bay

annual geometric

mean TN

long term geometric

mean TNNutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 34 July 2010 Figure 16

. Trend of annual geometric means for chlorophyll a in Choctawhatchee Bay, from IWR dataset

, 1996

– 2009, and long

- term geometric mean.

Figure 17. Comparison of a nnual geome tric means for TP for Choctawhatchee Bay regions based on salinity, from IWR dataset

, 1996

–

2009. 0 20 40 60 80 100 120 140

1994 1996 1998 2000 2002 2004 2006 2008 2010 

## Comparison of TP Geometric Means Choctawhatchee Bay Regions

East CB TP

River Mouth TP

Middle CB TP

West CB TP 0 0.5

1 1.5

2 2.5

3 3.5

4

1995 2000 2005 2010 

## Annual Geometric Means Chl a Choctawhatchee Bay

annual geometric
mean chl a

long term geo meanNutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 35 July 2010 Figure 18. Comparison of annual geometric means for TN for Choctawhatchee Bay regions based on salinity, from IWR dataset

, 1996

–

2009.

Figure 19. Comparison of annual geometric means for chlorophyll a for Choctawhatchee Bay regions based on salinity, from IWR dataset

, 1996

–

2009. 0 100 200 300 400 500 600 700 800 900

1995 2000 2005 2010 

## Comparison of TN Geometric Means Choctawhatchee Bay Regions

East CB TN

River Mouth CB TN

Middle CB TN

West CB TN

0 1 2 3 4 5 6

1996 1998 2000 2002 2004 2006 2008 2010 

## Comparison of Chl a Geometric Means Choctawhatchee Bay Regions

East CB CHL A

River Mouth CB CHL A

Middle CB CHL A

West CB CHL ANutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 36 July 2010 A significant factor in Choctawhatchee Bay’s water quality is high t urbidity resulting from the large
sediment l oad of the Choctawhatchee River. Table 14 summarizes m ean surface and bottom turbidity
for a 10

- year sampling period (2000

– 09) ( Lazzarino and Terrell 2010).

Table 1 4. Mean surface and bottom turbidity for Choctawhatchee Bay salinity

- based regions, 2000

– 09 (from
Lazzarino and Terrell 2010). Mean (STD) Wes tern Middle Eastern Surface Turbidity (NTU) 4(18) 11(64) 13(37) Bottom Turbidity (NTU) 6(21) 16(69) 18(41)



### Waters on the 303(d) List

N o i mpaired waters within the Choctawhatchee Bay Planning Unit on the Cycle 2 Verified List (2010) are
listed for nutrients or DO (FDEP 2010a)

. Table 15 lists the w aterbodies proposed for delisting. In the Choctawhatchee Bay Planning Unit

, waters are listed as impaired for the following parameters: mercury (in fish tissue), bacteria, and fecal coliform bacteria

.

Table 15. Waterbodies in the Choctawhatchee Bay Planning Unit proposed for DELISTING from the 1998 303(d) list for either nutrients or DO (FDEP 2010b). Waterbody Name Type WBID Impairment(s) Joe’s Bayou Estuary 906 Nutrients (historic chlor ophyll a ) Choctawhatchee Bay (Middle Segment 2) Estuary 778C DO , n utrients (chlorophyll a , historic chlorophyll a ) Choctawhatchee Bay

(Upper Segment) Estuary 778D Nutrients (historic chlorophyll a )

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.

The use of fecal coliforms as indicators of the presence of human pathogens has been under scrutiny in Florida for the past decade. One of the priorities of the Gulf of Mexico Alliance (GOMA) is to improve microbial source tracking (MST) and pathogen detection methods for use under Gulf of Mexico conditions (GOMA 2009). The GOMA Pathogens Workgroup recently submitted comments regarding the status of EPA recreational water quality criteria (GO MA 2009). The workgroup expressed concern that the EPA recreational criteria were derived in places that do not represent Gulf of Mexico conditions, and that the use of fecal indicators was not appropriate for waters primarily influenced by animal

sources . Areas in the Gulf of Mexico for which the workgroup thought the EPA criteria might not be appropriate included low

- population

- density coastal areas, areas of heavy rainfall, subtropical latitudes, and areas where waters contain a large amount of organic detritus material and/or colored dissolved organic matter (CDOM ) ( GOMA 2009). Choctawhatchee Bay falls into several of these categories: heavy rainfall, subtropical latitude, and large amounts of organic detritus/CDOM.

Boehm et al. (2009) express simi lar concern about the current and proposed recreational criteria, and specifically call attention to the need for further research and revision in tropical waters and waters adversely impacted by urban runoff and animal feces. FDEP recognizes that fecal c oliform andNutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 37 July 2010 enterococci bacteria may indicate a human source , or may co

- occur with anthropogenic nutrient inputs

, but there is ample evidence to caution against assuming that the presence of these bacteria automatically indicate s the presence of anthropogenic nutrients.

The following text is excerpted from a review conducted by Dr. V. J. Harwood of the University of South
Florida (USF) as part of a n MST project she is conducting for F DEP:

The main groups of indicator bacteria for recreational water quality assessment in use today include fecal coliforms, or a specific member of that group, Escherichia coli, in fresh water and the genus Enterococcus in both fresh and estuarine/marine waters. However, in order for the indicator concept to work optimally there are many assumptions that must hold true. One of the most important assumptions is that
indicator bacteria must co

- occur with human pathogens when pathogens are present and pose a human health risk. Unfortunately, recent research has indicated that this assumption is often false by showing that the presence of indicator bacteria do not always correlate well with the presence of pathogens such a s Salmonella

, Campylobacter

, Cryptosporidium

, Giardia , or enteric viruses ( Anderson et al. 2005 ; Bonadonna et al. 2002 ; Harwood et al. 2005 ; Lemarchand and Lebaron 2003 ; Lund 1996 ; Rees et al. 1998 ).

One important reason for the lack of correlation between traditional fecal indicator bacteria and pathogens is that the indicator bacteria are not specific to humans, nor to other hosts known to shed human pathogens in their feces, but are present in the intestines of all warm

- blooded animals and some cold

- bloo ded animals ( Souza et al.

1999 ). Because not all animals are equally likely to carry human pathogens, contamination from all sources does not represent an equal health risk. Thus, some sources of fecal contamination in water are of greater concern than o thers. Furthermore, there is increasing evidence of naturalized or environmentally adapted strains indicator bacteria (both coliforms and enterococci) that are capable of persisting in a culturable form for extended periods, or even growing, in a wide var iety of environmental matrices, including terrestrial soils, aquatic sediments, and attached to aquatic vegetation (Byappanahalli and Fujioka 1998

, Byappanahalli et al. 2003

, Ishii et al. 2006

, Jeng et al. 2005

, Ksoll et al. 2007

, Solo

- Gabriele et al. 2000

, Topp et al. 2003

, Whitman et al. 2003 ). If indicator bacteria are persisting in environmental matrices

, their reintroduction into the water column, which may occur during storms or high recreational activity, may lead to false positive indications regarding contamination and public health risk. As a result of these two confounding factors, it is now clear that simply measuring concentrations of waterborne indicator bacteria do not offer detailed enough information to properly determine health risks asso ciated with recreational

water use. Furthermore, this practice does not allow specific sources of contamination to be identified or targeted for remediation of water quality.



### Numeric Nutrient Criteria Recommendation

Relationship between Anthropogenic Nutrient Inputs and Adverse Biological Effects

There is considerable evidence to demonstrate that the nutrient regime in Choctawhatchee Bay is not adversely affecting biological condition. A reduction in nutrients would not lead to recovery of seagrassNutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 38 July 2010 beds or tidal marshes, or improve the condition of biological resources in the b ay. FDEP therefore

proposes nutrient concentration targets that reflect the current conditions as reported from 1974 to 2009 water quality monitoring data.

Proposed Numeric Nutrient and Chlorophyll 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 ca use

- effect relationship, the magnitude may be set at a level designed to maintain the current data distribution, accounting for natural temporal variability, when the current conditions are protective of the designated uses of the waterbody. Since a crite rion derived based on the existing data distribution has no direct link to any observed cause and effect relationship, it is assumed that maintaining the current data distribution will preserve the uses associated with that distribution.

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

the reference condition data distribution. Specifically, these components should be part of a statistical test designed to determine whether the long

- term distribution of data has shifted upward ( or in some cases, downward) from the reference distribution. This test would then be used to determine whether future monitoring data are consistent with the magnitude (long

- term average) defined by the 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 Choctawhatchee Bay is d escribed briefly below. More details concerning the statistical approaches

used can be found in the document Overview of FDEP Approaches for Nutrient Criter ia 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 distributio n, 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 inc rease 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 establishedNutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 39 July 2010 that a ten percent change in a water quality parameter represents an insignificant departure from the
historical condition, known as a de minimus change (US Sixth Circuit Court 2008). Therefore, the long

term geometric mean limit was derived to allow for up to a ten percent increase in the long

- term geometric mean, which was calculated as the geometric mean of the annual geometric means of the long

- term dataset fo r 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 basi s. 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 suff iciently robust cause

- effect relationship has demonstrated that a eutrophic response occurs over such timeframes. If however, such a short

term response cannot be demonstrated, or there is no indicati on 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 unaccepta bility 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

a pplication 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 a ssessment period, FDEP derived criteria expressed as an annual geometric mean by using the 75 th 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 gi ven segment.Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 40 July 2010 The two expressions of magnitude differ in the handling of within

- segment spatial variability. The network average magnitude was calculated based on the distribution of spatially averaged annual geometric means, while the single site magnit ude 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 r elatively homogeneous. I f 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 Propo sed 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) a n 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 Choctawhatchee Bay , as well the annual limits for each segment, are provided in Table 16.

Table 16 . Proposed numeric nutrient criteria for all segments of Choctawhatchee 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. N/A=Not ap plicable, because d ata were not sufficient for this analysis; criteria not yet proposed for
segment Total Phosphorus ( μ g/L)

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)

West 17 19 28 30

Central 16 18 25 26

East 23 25 26 27 Baywide 18 19 26 29 Total Nitrogen ( μ g/L)

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)

Central 373 410 516 523Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 41 July 2010 Middle 342 376 452 460

East 399 439 447 453 Baywide 370 407 502 514 Chlorophyll a (ug/L)

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)

West 3.59 3.95 5.18 5.31

Central 2.84 3.12 3.64 3.71

East N/A N/A N/A N/A Baywide 2.93 3.22 4.26 4.79Nutrient Criteria Technical Support Document Choctawhatchee Bay

Draft 42 July 2010 References Alexander, S

. 2010. Choctawhatchee Bay. A presentation to the Pensacola public workshop, February 10, 2010, in support of the development of numeric nutrient criteria in Florida estuaries and
coastal waters. Available: http://www.dep.s tate.fl.us/water/wqssp/nutrients/estuarine.htm

.
Anderson , K.L.

, J.E. Whitlock , and V.J. Harwood

. 2005

. Persistence and differential survival of fecal indicator bacteria in subtropical waters and sediments. Applied and Environmental Microbiology 71:3041

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