3/15/2010 0

Choctawhatchee Bay

Blake Schaeffer, Ph.D.

U.S. Environmental Protection Agency

Robert J. Livingston, Ph.D. 

Florida State University

Shelley Alexander

Northwest Florida Aquatic Preserve 
Office of Research and Development

National Health and Environmental Effects Research Laboratory, Gulf Ecology Division 1

Overview

• Blake Schaeffer

–Description/History

–Land Use/Land Cover

–N Yield and N Budget

–Optics and Remote Sensing

• Skip Livingston

–Impacts of anthropogenic nutrient 

loading

• Shelley Alexander

–Effects of nutrients on seagrass
Office of Research and Development

National Health and Environmental Effects Research Laboratory, Gulf Ecology Division 

Photo image area measures 2” H x 6.93” W and can be masked by a 

collage strip of one, two or three images.

The photo image area is located 3.19” from left and 3.81” from top of page. 

Each image used in collage should be reduced or cropped to a maximum of 

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accompanying images.

March 15, 2010

Blake Schaeffer, Jeff Jackson

US EPA, Gulf Breeze, FL

Choctawhatchee Bay

Photos: basinalliance.org
Office of Research and Development

National Health and Environmental Effects Research Laboratory, Gulf Ecology Division 3

Description of Choctawhatchee 

Bay

• Counties: Holmes, Washington, Okaloosa 

and Walton

• Cities: Destin, DeFuniak Springs, and 

Niceville 

• Area: 340 km2

• Mean depth: 3.8 m

• Watershed: 13x103 km2

– 91% of which is Choctawhatchee River 

• Salinity range 0 to 32
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National Health and Environmental Effects Research Laboratory, Gulf Ecology Division 4

Choctawhatchee Bay 1992-2007 Seagrass Coverage
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National Health and Environmental Effects Research Laboratory, Gulf Ecology Division 5

Historical Perspective

• Broad floodplain with seasonal flooding

– 13 major floods of Choctawhatchee River in last century

• 4th longest river in Florida and 3rd largest in annual discharge

• Rivers and tributaries receive ground water from springs of Florida 

Aquifer.

• Home to:

– Okaloosa darter

• U.S. Fish and Wildlife 

• Proposed to reclassify Endangered->Threatened

– Gulf sturgeon

• Combined population growth of surrounding counties was 23% in 10 

years from 2000 Census.

• Source: Northwest FL Water Management District
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National Health and Environmental Effects Research Laboratory, Gulf Ecology Division 6

Choctawhatchee Bay Watershed

Land-Use/Land-Cover

• Choctawhatchee Watershed Florida land use, 

cover and form classification system 

(FLUCC)

5x103 km2 (43.2% – Upland Forests)

2x103 km2 (20.1% - Agriculture)

2x103 km2 (15.7% - Wetlands)

1x103 km2 (10.3% - Rangeland)

862 km2 ( 6.2% - Urban and Built Up)

498 km2 ( 3.6% - Water)

56 km2 ( 0.4% - Barren Land)

58 km2 ( 0.4% - Transport, Utilities, etc)

13x103 km-2 Total
Office of Research and Development

National Health and Environmental Effects Research Laboratory, Gulf Ecology Division 7

Nitrogen Input Budget for Choctawhatchee Bay - estimated via 

USGS regional SPARROW model

• TN loading rate for Choctawhatchee Bay:

1x106 kg N y-1 (41% - Atmospheric Deposition)

1x106 kg N y-1 (31% - Fertilizer)

7.9x105 kg N y-1 (19% - Manure)

1.9x105 kg N y-1 ( 5% - Urban)

1.3x105 kg N y-1 ( 3% - Point Sources)

4x106 kg N y-1 (Total)
Office of Research and Development

National Health and Environmental Effects Research Laboratory, Gulf Ecology Division 8

Nitrogen Input Budget for Choctawhatchee Bay –

estimated via USGS regional SPARROW model

• TN loading rate for Choctawhatchee Bay:

3x106 kg N y-1 (94.3% - Choctawhatchee River)

7.6x104 kg N y-1 ( 1.9% - Lafayette Creek)

6.3x104 kg N y-1 ( 1.6% - Alaqua Creek)

3.5x104 kg N y-1 ( 0.9% - Rocky Creek)

3.2x104 kg N y-1 ( 0.8% - Turkey Creek)

1.7x104 kg N y-1 ( 0.4% - Basin Creek) 

8x103 kg N y-1 ( 0.2% - Swift Creek)

4x106 kg N y-1 Total

• 3x106 kg N y-1 Monitored TN loading from the Choctawhatchee River 

from 1999-2004.
Office of Research and Development

National Health and Environmental Effects Research Laboratory, Gulf Ecology Division 9

Total Nitrogen Yield from Choctawhatchee Bay Watershed -

estimated via USGS regional SPARROW model

• Estimate of TN yield for watershed is 

314 kg/km2/y.

• Ag sources, including Fertilizer and 

Manure are the largest anthropogenic 

sources in the watershed, accounting 

for 50% of total inputs.

• Anthropogenic sources in watershed 

contribute 58% of TN loading.

kg km-2 y-1
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National Health and Environmental Effects Research Laboratory, Gulf Ecology Division 10

Optics and Remote Sensing
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National Health and Environmental Effects Research Laboratory, Gulf Ecology Division 11

Optics and Remote Sensing
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IMPACTS OF ANTHROPOGENIC NUTRIENT 

LOADING IN COASTAL SYSTEMS OF 

THE EASTERN GULF OF MEXICO

Choctawhatchee Bay

Dr. Robert J. Livingston, Professor Emeritus 

Department of Biological Science

Florida State University

Tallahassee, Florida 32306

Email: livingstonr@comcast.net
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River flow rates of major systems in NE Gulf Region
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Nutrient loading characteristics of river 

systems in the eastern Gulf of Mexico. Data 

are mean values of monthly sampling over 

21 month period during years noted below.
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Comparison of physical/chemical water and 

sediment factors in highly productive upper 

bay areas

Data were taken during July in the various 

bays
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Comparison of plankton assemblages 

before and after anthropogenic nutrient 

loading in upper Perdido Bay
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Averaged data showing trophic organization of bays in NE Gulf of 

Mexico. Data include herbivores, omnivores, C1 carnivores, C2 

carnivores, and C3 carnivores that represent biomass of Fishes, 

infauna, and epibenthic invertebrates (FII) taken per m2 at upper bay 

stations monthly over the periods indicated.
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CHOCTAWHATCHEE BAY 

• Human activities associated with urbanization (e.g., storm water runoff and sewage 

spills) have contributed to the deterioration of the Choctawhatchee Bay system.

• The combination of nutrient loading and salinity stratification contributed to 

periodically severe water quality problems (hypoxia, anoxia) and associated 

reductions of natural productivity in affected sections of the bay.

• Continued urban development in western sections of the bay has been associated 

with increased urban stormwater runoff and sewage leaks leading to advanced 

hypereutrophication( hypoxia at depth, fish kills, mammal deaths) and reduced 

secondary production along with novel extensive red tide (Karenia breve) blooms in 

bay and offshore areas.

•

• There was a serious problem in the form of the deaths of sea turtles and hundreds of 

“bottlenose dolphins” in the Choctawhatchee system and along the coast between 

Choctawhatchee Bay and St. Andrews Bay. Deaths of some fish-eating terrestrial 

mammals such as raccoons and foxes in the region were also observed.

• Long-term, ecosystem-level studies of the Choctawhatchee system are needed to 

determine the extent of the bloom impacts and to devise effective management of the 

nutrient loading problems in the bay. Both river loading and urban bayou runoff 

should be the focus of any such studies. 
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Factors Sampled in Field Studies of 

Choctawhatchee River-Bay System (1985-

1989)

A detailed, ecosystem-level analysis was carried out in the Choctawhatchee River and 

Bay by our research group. The following factors were analyzed.

• River flow, rainfall

• Salinity, conductivity, temperature, dissolved oxygen,oxygen anomaly, pH, Secchi

• Water quality and loading nutrients: NH3, NO2, NO3, TIN, PON, DON, TON, TN, 

PO4, TDP, TIP, POP, DOP, TOP, TP. 

• Other water quality factors: DOC, POC, TOC, IC, TIC, TC, BOD. SiO2, TSS, 

TDS, DIM, DOM, POM, PIM. NCASI color, turbidity, Chlorophyll a, 

• Water/sediment pollutants (metals)

• Submerged aquatic vegetation analyses (quadrats) and transplants

• Whole water and net phytoplankton (nets, whole water)

• Infaunal macroinvertebrates (ponars, cores)

• Invertebrates (seines, trawls)

• Fishes (seines, trawls)

• Food web transformations (based on stomach contents of fishes and invertebrates)

•
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Choctawhatchee River

Water quality data, together with the conductivity levels, indicate periodic deterioration in Pine 

Log Creek, Seven Run Creek, Bruce Creek, and Wright's Creek. Clear cutting and sewage 

discharges were noted in various parts of the drainage, but water quality in the main river was 

generally good.

• Riverine phytoplankton abundance in the Choctawhatchee system is associated with stream

size, flow rates, and possibly the wetlands vegetation. The abundance of microalgae in the

main channel stations was low relative to most of the river tributaries

There was a basic dichotomy of habitat distribution between the various tributaries of the 

system and the main stem of the river. Spatial and temporal river flow and water quality 

differences were noted in addition to differences of sediment characteristics.

• Infaunal macroinvertebrates were comparatively depauperate in numbers and species richness 

in the main stem of the river.

•

• Temporal differences in the distribution of epibenthic macroinvertebrates were noted between 

the tributaries and the main channel. The fishes were fewer in number and species richness in 

the tributaries than the main stem. Such basic differences in fish assemblages were ascribed to 

varying patterns of habitat distributions.

•
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Nutrient loading, bay habitat 

response and associated 

food web disruptions • The Choctawhatchee Bay system is a large, highly complex series of habitats that is strongly influenced by 

freshwater input (river, bayou drainages), the single entrance to the gulf (East Pass), and the physiographic 

structure of the bay. These have combined to cause low turnover rates, vertical salinity stratification in central 

and western sections, and associated habitat deterioration due to hypoxia/anoxia.

• High salinities and associated stratification accompanying the opening of East Pass nearly a century ago 

together with various other human activities (urbanization, storm water runoff, sewage dischrages) have 

contributed to the deterioration of the natural aquatic resources in the bay.

• Critical, highly productive habitats include the few remaining estuarine wet-lands (emergent vegetation), the 

shallow submerged aquatic vegetation (Halodule beds), the river mouth (and associated freshwater wetlands), 

and the various (unpolluted) bayous.

• Although river loading of various nutrients was relatively high compared to other systems, the primary 

problem of anthropogenic nutrient loading appeared to be centered in urban lagoons. For example, the 

situation in Old Pass Lagoon combines loading of nutrients and organic matter and a lack of flushing to cause 

water quality problems (hypoxia, anoxia) and associated reductions of natural productivity. This has led to 

high nutrients (N, P) in the water column, silt-laden sediments, high phytoplankton productivity, low numbers 

of herbivores (zooplankton, meroplankton), a depauperate infaunal invertebrate community and relatively few 

epibenthic invertebrates and fishes. 

• The Old Pass Lagoon conditions are typical of a number of the urban lagoons in the bay. This situation is also 

found in parts of the western bay areas affected by high salinity stratification. 

• The relationship of nutrient concentration and nutrient loading remains complex, and this aspect of the cause 

of damaging blooms needs to be examined. 

•
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Salinity stratification and bottom hypoxia: The opening of East Pass in the 

early 20th century allow salt water to infiltrate the bay. This has led to periodic 

salinity stratification, isolation of the bottom waters from surface interactions, 

and reduced dissolved oxgyen in affected parts of the bay. This represents 

one reason for the relatively low benthic productivity of the bay. 
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Comparison of dissolved oxygen conditions in Alaqua 

Bayou (C9) and Garnier Bayou (C40)
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Project: Phytoplankton from Choctawhatchee Bay, Florida (Poquito Bayou Mouth, 

Hand’s cove, Garnier Bayou, South Shalimar yacht Club, Chula Vista Bayou, Marker 

61, East Pass.

Date of Collection: 04-04-2006

Date received:04-05-2006

• A.K.S.K. Pasad

• A potentially harmful diatom, Pseudonitzschia (possibly pseudodelicatissima) sp.

was

• present in almost all of the stations examined. Cyclotella choctawhatcheeana and

• Chaetoceros laevis were also present. Dinoflagellates, Prorocentrum triestinum,

• Prorocentrum micans and Prorocentrum cordatum (syn. P. minimum) were present

• in low numbers. All three species are known to form red tide discolorations. 

• According to Manual of Harmful Marine Microalgae (Hallegraeff et al. 2003), 

• increasing numbers of Pseudonitzschia species are being found to produce 

• domoic acid, a toxin that causes Amnesic Shellfish poisoning (ASP).

• Karenia brevis was not observed

• There has not been a systematic analysis of the phytoplankton assemblages of the 

bay. The primary concern with red tide (Karenia brevis) ignores the inportance of 

other bloom species that can have major adverse effects on bay food webs.
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Adverse Effects of nutrients on 

Seagrass Distribution in 

Choctawhatchee Bay 

Presented by:

Shelley Alexander

Northwest Florida Aquatic Preserve 
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Coverage of Seagrass between 1992-2003 from 

USGS aerials
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Western Choctawhatchee Bay 1992-2003 

seagrass coverage change
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Uncorrected chl a values East Choctawhatchee Bay 

ug/l
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Uncorrected chl a values for West Choctawhatchee Bay

ug/l
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Contributing factors to decline in Seagrass

coverage within Choctawhatchee Bay

• Historical algal blooms caused by over 

nutrification from STP and NPS

• One year flushing time

• Sediment quality (chemical contamination 

and high organic silts)