Executive Summary (revised)

This report was prepared by the Charlotte Harbor National Estuary Program (CHNEP) and local scientists for FL

Department of Environmental Protection (FDEP), to support the development of numeric nutrient criteria for the 

estuaries comprising the CHNEP. The primary purpose of the proposed numeric nutrient criteria is to protect healthy, 

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

CHNEP is located in southwest Florida in the eastern Gulf of Mexico and is the second largest estuarine system in Florida, 

encompassing over 735 km2

. Eight interconnected estuaries, bays and lagoons, 3 major river systems and over 20 tidal 

creeks form a series of unique waterbodies with defining bathymetry, Gulf-riverine connections, land:water ratios and 

resource management challenges. These individual estuaries include: Dona/Roberts Bays, Lemon Bay, Charlotte 

Harbor/Cape Haze, Tidal Myakka River, Tidal Peace River, Pine Island Sound/Matlacha Pass, Tidal Caloosahatchee River, 

and San Carlos/Estero Bays. Six of these estuaries are Florida Aquatic Preserves. The CHNEP watershed is greater than 

12,000 km2

Primary emergent and submerged habitats within the CHNEP include: mangroves (>24,000 hectares), submerged 

aquatic vegetation (>24,000 hectares), saltmarsh (>5,000 hectares), oysters (>100 hectares), and invertebrate rich interand sub-tidal mudflats and sand bars. These habitats support over 385 fish species, 330 bird species, and listed species 

including small tooth sawfish, manatee, American crocodile, bald eagle, and wood stork. 

, supporting over 1.2 million people, concentrated in the fragile coastal corridor which is subject to potential 

sea level rise effects. The watershed includes a great diversity of land uses, including about 45% open lands (pasture, 

range, forests), 25% wetlands and freshwater, 15% urban, 10% agriculture and 5% extractive mining. Most of the 

estuary and island shoreline (>45%) is set aside as conservation land through national, state, local & nonprofit programs. 

Seagrass distribution varies temporally and spatially throughout the CHNEP. From 1945 to 1999 seagrass acres 

decreased about 35%. Anthropogenic affects of decreased water clarity (due to increased nutrient loadings), alteration 

of freshwater inflows, and dredge and fill activities (i.e. Intracoastal Waterway and Sanibel bridge causeway) contributed 

to the losses. In the last decade, seagrass distribution has stabilized overall, but responds to seasonal and annual 

changes in rainfall. CHNEP recently adopted seagrass protection and restoration targets for each estuary, totaling 

25,100 hectares for protection and 1,600 hectares for restoration. Water clarity targets have been developed for each 

CHNEP estuary based on seagrass light requirements and key light attenuating factors (color, chlorophyll a and 

turbidity). 

Chlorophyll, nitrogen, phosphorus and dissolved oxygen conditions vary spatially and temporally throughout the 

estuarine waters of the CHNEP. Donna/Roberts and Lemon Bays are not impaired for chlorophyll or dissolved oxygen, 

and appear to have decreasing nitrogen conditions, with some areas of increasing phosphorus. Pine Island Sound, 

Matlacha Pass, Tidal Caloosahatchee River, San Carlos Bay and Estero Bay are also not impaired for chlorophyll (some 

tidal tributaries are) or dissolved oxygen, but show some increases in nitrogen with some decreases in phosphorus 

levels. The remaining three estuaries, Tidal Myakka River, Tidal Peace River and Upper Charlotte Harbor, have 

chlorophyll impairments, with some increases in nitrogen and phosphorus. Bottom water hypoxia has been 

documented in Charlotte Harbor, but the extent and duration varies, making it difficult to distinguish between natural 

and anthropogenic causes. However, these 3 estuaries are not listed for dissolved oxygen impairments. Additional 

evaluation of chlorophyll, dissolved oxygen and nutrient trends, concentrations and loadings is currently being 

undertaken by the CHNEP, to be completed in fall 2010. The results will be used to develop nutrient targets that 

support the water clarity and seagrass targets for each CHNEP estuary.

The regional biological data suggests that the designated aquatic life uses are being fully supported throughout the 

CHNEP. However, the CHNEP seagrass targets identify some seagrass restoration needs in 7 of the 8 CHNEP estuaries, 

ranging from about 1% to 50% , especially in the Tidal Myakka River, Dona/Roberts Bays, Matlacha Pass and Estero Bay. 

Restoration schemes will vary by estuary, but will include both improvements in hydrologic as well as water quality 

conditions to restore natural salinity, color, and dissolved oxygen levels, as well as nutrients. 

Contributors: Dr. Lisa Beever (CHNEP), Mr. Tony Janicki (Janicki Environmental), Ms. Judy Ott (CHNEP), Mr. Phil Stevens 

(FWC) and Mr. Mike Wessel (Janicki Environmental). 
Response Variable Dona & Roberts Bays Lemon Bay Myakka River Peace River Charlotte Harbor & Cape Haze Pine Island Sound & Matlacha Pass

Tidal Caloosahatche River & San Carlos 

Bay Estero Bay

Observed Historically or Currently? No No Possibly Yes Yes No No No

Explanation Not listed as impaired for DO. Not 

enough data to establish trends.

Not listed as impaired for DO. One of 6 

stations has improving trends.

Not listed as impaired for DO, however, 

the decreasing trends in 2 of 10 

stations.

Recurrent wet season bottom water 

hypoxia documented in numerous 

studies. Surface water is not listed as 

impaired for DO. Several stations in 

tidal Peace show improving trends.

Recurrent wet season bottom water 

hypoxia documented in numerous 

studies. Surface water is not listed as 

impaired for DO. Some improving 

trends.

Not listed as impaired for DO. 

Improving trends are shown 

throughout.

Not listed as impaired for DO. 

Improving trends in San Carlos Bay. No 

trends in Caloosahatchee.

Not listed as impaired for DO. Some 

improving trends.

Source CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

Turner et. al. Paleo-indicators & water 

quality change in the Charlotte Harbor 

Estuary, 2006. SWFWMD Charlotte 

Harbor SWIM Plan, 2000. Camp, 

Dresser & McKee Study of Seasonal & 

Spatial Patterns of Hypoxia in Upper 

Charlotte CHNEP, 1998. Maps of FDEP 

303(d) listing of impairments, 2010. 

CHNEP/Janicki Water Quality Data 

Analysis & Report for CHNEP, 2007.

Turner et. al. Paleo-indicators & water 

quality change in the Charlotte Harbor 

Estuary, 2006. SWFWMD Charlotte 

Harbor SWIM Plan, 2000. Camp, 

Dresser & McKee Study of Seasonal & 

Spatial Patterns of Hypoxia in Upper 

Charlotte CHNEP, 1998. Maps of FDEP 

303(d) listing of impairments, 2010. 

CHNEP/Janicki Water Quality Data 

Analysis & Report for CHNEP, 2007. 

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

Observed Historically or Currently? Yes Yes, upper Lemon Bay Yes No No. No No. No

Explanation Water clarity trends down, based on 

sechhi depth.

Water clarity trends down in upper 

Lemon Bay for 2 of 5 stations, based on 

sechhi depth. No trends for both Lower 

Lemon Bay stations.

Water clarity trends down in 2 of 5 

stations, based on sechhi depth. 

 No secchi depth trends for the four 

stations in the tidal Peace River. Mixed 

results in the freshwater tributaries.

 No secchi depth trends for the station 

in Charlotte Harbor.

 No secchi depth trends for both 

stations in Matlacha Pass.

Secchi depth improvement in 2 of 3 

stations in San Carlos Bay.

Secchi depth improvement for the 

station in Matazas Pass..

Source CHNEP/Janicki Water Quality Data 

Analysis & Report for CHNEP, 2007. 

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 3: Water 

Clarity Target development, 2009 

established methods only. Additional 

analysis pending from Janicki 

Environmental, Inc. 

CHNEP/Janicki Water Quality Data 

Analysis & Report for CHNEP, 2007. 

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 3: Water 

Clarity Target development, 2009 

established methods only. Additional 

analysis pending from Janicki 

Environmental, Inc. 

CHNEP/Janicki Water Quality Data 

Analysis & Report for CHNEP, 2007. 

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 3: Water 

Clarity Target development, 2009 

established methods only. Additional 

analysis pending from Janicki 

Environmental, Inc. 

CHNEP/Janicki Water Quality Data 

Analysis & Report for CHNEP, 2007. 

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 3: Water 

Clarity Target development, 2009 

established methods only. Additional 

analysis pending from Janicki 

Environmental, Inc. 

CHNEP/Janicki Water Quality Data 

Analysis & Report for CHNEP, 2007. 

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 3: Water 

Clarity Target development, 2009 

established methods only. Additional 

analysis pending from Janicki 

Environmental, Inc. 

CHNEP/Janicki Water Quality Data 

Analysis & Report for CHNEP, 2007. 

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 3: Water 

Clarity Target development, 2009 

established methods only. Additional 

analysis pending from Janicki 

Environmental, Inc. 

CHNEP/Janicki Water Quality Data 

Analysis & Report for CHNEP, 2007. 

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 3: Water 

Clarity Target development, 2009 

established methods only. Additional 

analysis pending from Janicki 

Environmental, Inc. 

CHNEP/Janicki Water Quality Data 

Analysis & Report for CHNEP, 2007. 

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 3: Water 

Clarity Target development, 2009 

established methods only. Additional 

analysis pending from Janicki 

Environmental, Inc. 

Observed Historically or Currently? Insufficent data. Insufficient data. Insufficient data. Insufficient data. No Yes Yes Insufficient data.

Explanation Spatial analysis of red tide between 

1954-1963 and 1994-2003 suggests 

Charlotte Harbor one of few places Red 

Tide has decreased.

Trichodesmium and Lyngya blooms in 

estuaries (Pine Island Sound, San Carlos 

Bay)

Blue-green algae blooms in river – 

predominately Microcystis in recent 

years (could shift to other species e.g. 

Anabaena, Cylindrospermopsis, etc.)

Source Larry Brand, University of Miami. Caloosahatchee River Watershed 

Existing Water Quality Monitoring 

Inventory and Hot Issues List for 

Caloosahatchee River Estuary, 2008

Caloosahatchee River Watershed 

Existing Water Quality Monitoring 

Inventory and Hot Issues List for 

Caloosahatchee River Estuary, 2008

CHNEP Estuary Segment

Table 1a. Checklist of nutrient enrrichment symptoms for each estuary within the CHNEP watershed (revised).

Low dissolved oxygen (DO) (hypoxia/anoxia):

Reduced clarity:

Phytoplankton blooms (nusiance or toxic):
Response Variable Dona & Roberts Bays Lemon Bay Myakka River Peace River Charlotte Harbor & Cape Haze Pine Island Sound & Matlacha Pass

Tidal Caloosahatche River & San Carlos 

Bay Estero Bay

CHNEP Estuary Segment

Table 1a. Checklist of nutrient enrrichment symptoms for each estuary within the CHNEP watershed (revised).

 

Observed Historically or Currently? Insufficient data. No Yes Yes No Yes, Matlacha only Unlikely Yes

Explanation No statistically signficant change. Some 

improvement measured.

Statistically significant (.001 level) 

increase of ephyphye load on 

seagrasses.

Statistically significant (.001 level) 

increase of ephyphye load on 

seagrasses.

No statistically signficant change in 

Gasparilla Sound and Upper West 

Charlotte Harbor but some 

improvement measured. Statistically 

significant (.05 level) decrease of 

ephyphye load on seagrasses Lower 

East Charlotte Harbor.

Statistically significant (.05 level) 

increase of ephyphye load on 

seagrasses in Matlacha Pass. No change 

in Pine Island Sound.

No statistically signficant change. Some 

degredation measured. Measures not 

taken in Tidal Caloosahatchee.

Epiphyte load heaviest of all strata as 

shown in report. Period of record 

begins in 2004, so not enough data to 

establish a trend.

Source No source of data. Dona and Robert’s 

Bay Second Annual Watershed and 

Estuary Analysis, 2004 reports 

epiphytes measured but no analyses 

are provided.

Seagrass Annual Data Summary from 

the Charlotte Harbor and Estero Bay 

Aquatic Preserve Seagrass Transect 

monitoring Program 1996-2006, 2007. 

Analysis of raw data by L. Beever, 2010.

Seagrass Annual Data Summary from 

the Charlotte Harbor and Estero Bay 

Aquatic Preserve Seagrass Transect 

monitoring Program 1996-2006, 2007. 

Analysis of raw data by L. Beever, 2010.

Seagrass Annual Data Summary from 

the Charlotte Harbor and Estero Bay 

Aquatic Preserve Seagrass Transect 

monitoring Program 1996-2006, 2007. 

Analysis of raw data by L. Beever, 2010.

Seagrass Annual Data Summary from 

the Charlotte Harbor and Estero Bay 

Aquatic Preserve Seagrass Transect 

monitoring Program 1996-2006, 2007. 

Analysis of raw data by L. Beever, 2010.

Seagrass Annual Data Summary from 

the Charlotte Harbor and Estero Bay 

Aquatic Preserve Seagrass Transect 

monitoring Program 1996-2006, 2007. 

Analysis of raw data by L. Beever, 2010.

Seagrass Annual Data Summary from 

the Charlotte Harbor and Estero Bay 

Aquatic Preserve Seagrass Transect 

monitoring Program 1996-2006, 2007. 

Analysis of raw data by L. Beever, 2010.

Seagrass Annual Data Summary from 

the Charlotte Harbor and Estero Bay 

Aquatic Preserve Seagrass Transect 

monitoring Program 1996-2006, 2007. 

Analysis of raw data by L. Beever, 2010.

Observed Historically or Currently? Insufficient data. Insufficient data. Insufficient data. Insufficient data. Insufficient data. Yes Insufficient data. Insufficient data.

Explanation Drift Algae (multiple species) – Has 

been a reported problem on beaches, 

seagrass beds, offshore reefs, and in 

shrimp nets offshore.

Source Caloosahatchee River Watershed 

Existing Water Quality Monitoring 

Inventory and Hot Issues List for 

Caloosahatchee River Estuary, 2008

Observed Historically or Currently? Yes Yes Unlikely Yes Yes, East and West Walls only Yes, Matlacha only Likely, Tidal Caloosahatchee only Yes

Explanation 19% loss of seagrasses between 1950 

and mean mapped coverage between 

1988 and 2006. Late 1960's drainage 

project more than tripled the 

watershed area, changing salinity and 

water clarity to the detriment of 

seagrass.

7% loss of seagrasses between 1950 

and mean mapped coverage between 

1988 and 2006. Most of loss found is in 

lower Lemon Bay.

Only one year (2004) within the six 

mapping years had a lower extent than 

the 1950's era map. No restoration 

target is set because of the 40% gain, 

however, it is acknowledged that highCDOM waters are difficult to map from 

aerials. 

60% loss of seagrasses between 1950 

and mean mapped coverage between 

1988 and 2006. It is acknowledged 

that high-CDOM waters are difficult to 

map from aerials. 

10% loss on East and West Walls. Cape 

Haze and Bookeelia segments show 

gains between 1950 and each of the 

six mapping years between 1988 and 

2006.

Matlacha had a 10% loss between1950 

and mean mapped coverage between 

1988 and 2006. However, extent has 

increased during every mapping year 

for both Pine Island Sound and 

Matlacha Pass.

No restoration target has been set for 

San Carlos Bay, which has increased in 

extent for every mapping year between 

1999 and 2006. 

Localized with seasonal & annual 

variability; some natural & some 

anthropogenic causes; related to 

dredge & fill activities & changes in 

salinity & water clarity (color, 

chlorphyll & turbitity).

Source CHNEP/Janicki Water Quality Target 

Refinement Interim Report 2: Seagrass 

Target Development, 2009. SWFWMD 

Seagrass Aerial Photography. Dona Bay 

Watershed Management Plan, 2007.

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 2: Seagrass 

Target Development, 2009. SWFWMD 

Sesagrass Aerial Photography. 

Boswell/SCCF "Seagrass Species 

Composition & Distribution Trends in 

Relation to Salinity Fluctuations in 

Charlotte Harbor, FL", 2006. FDEP 

"Seagrass Annual Data Summary from 

the Charlotte Harbor & Estero Bay 

Aquatic Preserves Seagrass Transect 

Monitoring Program 1999-2006, 2007.

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 2: Seagrass 

Target Development, 2009. SWFWMD 

Sesagrass Aerial Photography. 

Boswell/SCCF "Seagrass Species 

Composition & Distribution Trends in 

Relation to Salinity Fluctuations in 

Charlotte Harbor, FL", 2006. FDEP 

"Seagrass Annual Data Summary from 

the Charlotte Harbor & Estero Bay 

Aquatic Preserves Seagrass Transect 

Monitoring Program 1999-2006, 2007.

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 2: Seagrass 

Target Development, 2009. 

Boswell/SCCF "Seagrass Species 

Composition & Distribution Trends in 

Relation to Salinity Fluctuations in 

Charlotte Harbor, FL", 2006. FDEP 

"Seagrass Annual Data Summary from 

the Charlotte Harbor & Estero Bay 

Aquatic Preserves Seagrass Transect 

Monitoring Program 1999-2006, 2007.

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 2: Seagrass 

Target Development, 2009. 

SWFWMD& SFWMD Sesagrass Aerial 

Photography. Boswell/SCCF "Seagrass 

Species Composition & Distribution 

Trends in Relation to Salinity 

Fluctuations in Charlotte Harbor, FL", 

2006. FDEP "Seagrass Annual Data 

Summary from the Charlotte Harbor & 

Estero Bay Aquatic Preserves Seagrass 

Transect Monitoring Program 1999-

2006, 2007.

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 2: Seagrass 

Target Development, 2009. SFWMD 

Sesagrass Aerial Photography. 

Boswell/SCCF "Seagrass Species 

Composition & Distribution Trends in 

Relation to Salinity Fluctuations in 

Charlotte Harbor, FL", 2006. FDEP 

"Seagrass Annual Data Summary from 

the Charlotte Harbor & Estero Bay 

Aquatic Preserves Seagrass Transect 

Monitoring Program 1999-2006, 2007.

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 2: Seagrass 

Target Development, 2009. SFWMD 

Sesagrass Aerial Photography. 

Boswell/SCCF "Seagrass Species 

Composition & Distribution Trends in 

Relation to Salinity Fluctuations in 

Charlotte Harbor, FL", 2006. FDEP 

"Seagrass Annual Data Summary from 

the Charlotte Harbor & Estero Bay 

Aquatic Preserves Seagrass Transect 

Monitoring Program 1999-2006, 2007.

CHNEP/Janicki Water Quality Target 

Refinement Interim Report 2: Seagrass 

Target Development, 2009. SFWMD 

Sesagrass Aerial Photography. 

Boswell/SCCF "Seagrass Species 

Composition & Distribution Trends in 

Relation to Salinity Fluctuations in 

Charlotte Harbor, FL", 2006. FDEP 

"Seagrass Annual Data Summary from 

the Charlotte Harbor & Estero Bay 

Aquatic Preserves Seagrass Transect 

Monitoring Program 1999-2006, 2007.

Problematic macroalgal growth:

Submerged aquatic vegetation (SAV) community changes or loss:

Problematic epiphyte growth:
Response Variable Dona & Roberts Bays Lemon Bay Myakka River Peace River Charlotte Harbor & Cape Haze Pine Island Sound & Matlacha Pass

Tidal Caloosahatche River & San Carlos 

Bay Estero Bay

CHNEP Estuary Segment

Table 1a. Checklist of nutrient enrrichment symptoms for each estuary within the CHNEP watershed (revised).

 

Observed Historically or Currently? No No No Possibly No Possibly Possibly No

Explanation Over the years dredge-and-fill has 

eliminated about 25% of mangrove and 

significant areas of salt marsh 

throughout the study area. Nutrient 

pollution has not contributed 

significantly to this loss. 

Over the years dredge-and-fill has 

eliminated about 25% of mangrove and 

significant areas of salt marsh 

throughout the study area. Nutrient 

pollution has not contributed 

significantly to this loss. 

Over the years dredge-and-fill has 

eliminated about 25% of mangrove and 

significant areas of salt marsh 

throughout the study area. Nutrient 

pollution has not contributed 

significantly to this loss. Excess 

nutrients can change slat marsh 

vegetation, increasing cattails over bull 

rush and juncus.

Over the years dredge-and-fill has 

eliminated about 25% of mangrove and 

significant areas of salt marsh 

throughout the study area. Nutrient 

pollution has not contributed 

significantly to this loss. Excess 

nutrients can change slat marsh 

vegetation, increasing cattails over bull 

rush and juncus.

Over the years dredge-and-fill has 

eliminated about 25% of mangrove and 

significant areas of salt marsh 

throughout the study area. Nutrient 

pollution has not contributed 

significantly to this loss. 

Over the years dredge-and-fill has 

eliminated about 25% of mangrove and 

significant areas of salt marsh 

throughout the study area. Nutrient 

pollution has not contributed 

significantly to this loss. Excess 

nutrients can change slat marsh 

vegetation, increasing cattails over bull 

rush and juncus. Cattails are in evident 

associated with the North Spreader 

Waterway, adjacent to Matlacha Pass

Over the years dredge-and-fill has 

eliminated about 25% of mangrove and 

significant areas of salt marsh 

throughout the study area. Nutrient 

pollution has not contributed 

significantly to this loss. Excess 

nutrients can change slat marsh 

vegetation, increasing cattails over bull 

rush and juncus.

Over the years dredge-and-fill has 

eliminated about 25% of mangrove and 

significant areas of salt marsh 

throughout the study area. Nutrient 

pollution has not contributed 

significantly to this loss. Excess 

nutrients can change slat marsh 

vegetation, increasing cattails over bull 

rush and juncus.

Source CHNEP Comprehensive Conservation 

and Management Plan, 2008.

CHNEP Comprehensive Conservation 

and Management Plan, 2008.

CHNEP Comprehensive Conservation 

and Management Plan, 2008.

CHNEP Comprehensive Conservation 

and Management Plan, 2008.

CHNEP Comprehensive Conservation 

and Management Plan, 2008.

CHNEP Comprehensive Conservation 

and Management Plan, 2008.

CHNEP Comprehensive Conservation 

and Management Plan, 2008.

CHNEP Comprehensive Conservation 

and Management Plan, 2008.

Emergent or shoreline vegetation community changes or loss:
Response Variable Dona & Roberts Bays Lemon Bay Myakka River Peace River Charlotte Harbor & Cape Haze Pine Island Sound & Matlacha Pass

Tidal Caloosahatche River & San Carlos 

Bay Estero Bay

CHNEP Estuary Segment

Table 1a. Checklist of nutrient enrrichment symptoms for each estuary within the CHNEP watershed (revised).

 

Observed Historically or Currently? No No No No No No No No

Explanation No extensive hardbottom communit 

exists within the CHNEP estuaries. 

Vermitiid worm shell reefs found off 

barrier islands in Gulf of Mexico.

No extensive hardbottom communit 

exists within the CHNEP estuaries. 

Vermitiid worm shell reefs found off 

barrier islands in Gulf of Mexico.

No extensive hardbottom communit 

exists within the CHNEP estuaries. 

Vermitiid worm shell reefs found off 

barrier islands in Gulf of Mexico.

No extensive hardbottom communit 

exists within the CHNEP estuaries. 

Vermitiid worm shell reefs found off 

barrier islands in Gulf of Mexico.

No extensive hardbottom communit 

exists within the CHNEP estuaries. 

Vermitiid worm shell reefs found off 

barrier islands in Gulf of Mexico. Boca 

Grande Pass has limestone shelf 

exposures with corals.

No extensive hardbottom communit 

exists within the CHNEP estuaries. 

Vermitiid worm shell reefs found off 

barrier islands in Gulf of Mexico. Pather 

Isalnd Pass has limestone shelf 

exposures with intermittent corals.

No extensive hardbottom communit 

exists within the CHNEP estuaries. 

Vermitiid worm shell reefs found off 

barrier islands in Gulf of Mexico.San 

Carlos Pass off Punta Rass and Point 

Ybel has limestone shelf exposures 

with intermittent corals, on side 

seaward of the causeway.

No extensive hardbottom communit 

exists within the CHNEP estuaries. 

Vermitiid worm shell reefs found off 

barrier islands in Gulf of Mexico.

Source CHNEP/Mote Marine Laboratory 

Technical Report No. 1169: Benthic 

Invertebrate species Richness & 

Diversity at Different Habitats in the 

Greater Charlotte Harbor System, 2007

CHNEP/Mote Marine Laboratory 

Technical Report No. 1169: Benthic 

Invertebrate species Richness & 

Diversity at Different Habitats in the 

Greater Charlotte Harbor System, 2007

CHNEP/Mote Marine Laboratory 

Technical Report No. 1169: Benthic 

Invertebrate species Richness & 

Diversity at Different Habitats in the 

Greater Charlotte Harbor System, 2007

CHNEP/Mote Marine Laboratory 

Technical Report No. 1169: Benthic 

Invertebrate species Richness & 

Diversity at Different Habitats in the 

Greater Charlotte Harbor System, 2007

CHNEP/Mote Marine Laboratory 

Technical Report No. 1169: Benthic 

Invertebrate species Richness & 

Diversity at Different Habitats in the 

Greater Charlotte Harbor System, 2007

CHNEP/Mote Marine Laboratory 

Technical Report No. 1169: Benthic 

Invertebrate species Richness & 

Diversity at Different Habitats in the 

Greater Charlotte Harbor System, 2007

CHNEP/Mote Marine Laboratory 

Technical Report No. 1169: Benthic 

Invertebrate species Richness & 

Diversity at Different Habitats in the 

Greater Charlotte Harbor System, 2007

CHNEP/Mote Marine Laboratory 

Technical Report No. 1169: Benthic 

Invertebrate species Richness & 

Diversity at Different Habitats in the 

Greater Charlotte Harbor System, 2007

Observed Historically or Currently? Yes Yes No Yes Likely Yes, in Matlacha Pass Yes, in Caloosahatchee No

Explanation High diversity and Low abundance of 

benthic macro-invertebrates.

High diversity and low abundance of 

benthic macro-invertebrates.

Good diversity and high abundance of 

benthic macro-invertebrates.

Low diveristy and high abudannce of 

benthic macro-invertebrates.

High diversity in seagrass and low 

abudannce of benthic macroinvertebrates.

Good abundance in both Sound and 

Pass; high diversity in Sound and low in 

Pass of benthic macro-invertebrates..

Abundance of bethic macroinvertebrates highest found in 

literature, around San Carlos Bay. 

Abundance very low in 

Caloosahatchee.

High diversity and good anundance of 

benthic macro-invertebrates. 

Source CHNEP/Photo Science Historic Benthic 

Habitat Maps, 2006. CHNEP/Mote 

Marine Laboratory Technical Report 

No. 1169: Benthic Invertebrate species 

Richness & Diversity at Different 

Habitats in the Greater Charlotte 

Harbor System, 2007

CHNEP/Photo Science Historic Benthic 

Habitat Maps, 2006. CHNEP/Mote 

Marine Laboratory Technical Report 

No. 1169: Benthic Invertebrate species 

Richness & Diversity at Different 

Habitats in the Greater Charlotte 

Harbor System, 2007

CHNEP/Photo Science Historic Benthic 

Habitat Maps, 2006. CHNEP/Mote 

Marine Laboratory Technical Report 

No. 1169: Benthic Invertebrate species 

Richness & Diversity at Different 

Habitats in the Greater Charlotte 

Harbor System, 2007

CHNEP/Photo Science Historic Benthic 

Habitat Maps, 2006. CHNEP/Mote 

Marine Laboratory Technical Report 

No. 1169: Benthic Invertebrate species 

Richness & Diversity at Different 

Habitats in the Greater Charlotte 

Harbor System, 2007

CHNEP/Photo Science Historic Benthic 

Habitat Maps, 2006. CHNEP/Mote 

Marine Laboratory Technical Report 

No. 1169: Benthic Invertebrate species 

Richness & Diversity at Different 

Habitats in the Greater Charlotte 

Harbor System, 2007

CHNEP/Photo Science Historic Benthic 

Habitat Maps, 2006. CHNEP/Mote 

Marine Laboratory Technical Report 

No. 1169: Benthic Invertebrate species 

Richness & Diversity at Different 

Habitats in the Greater Charlotte 

Harbor System, 2007

CHNEP/Photo Science Historic Benthic 

Habitat Maps, 2006. CHNEP/Mote 

Marine Laboratory Technical Report 

No. 1169: Benthic Invertebrate species 

Richness & Diversity at Different 

Habitats in the Greater Charlotte 

Harbor System, 2007

CHNEP/Photo Science Historic Benthic 

Habitat Maps, 2006. CHNEP/Mote 

Marine Laboratory Technical Report 

No. 1169: Benthic Invertebrate species 

Richness & Diversity at Different 

Habitats in the Greater Charlotte 

Harbor System, 2007

Observed Historically or Currently? Yes - localized. Yes - localized. Yes - localized. Yes - localized. Yes - localized. Yes - localized. Yes - localized. Yes - localized.

Explanation Localized and no statistically significant 

increase. From 1972-2010 4 red 

tide/low DO fish kill events were 

reported (all from red tide), as well as 

others from cold weather & unknown 

causes.

Localized and no statistically significant 

increase. From 1972 - 2010 16 red 

tide/low DO fish kill events were 

reported (12 red tide & 4 DO), as well 

as others from cold weather & 

unknown causes. In 2008, a fish with 

tumors was found in Stump Pass. Of 

the fish disease categories, all were 

related to red tide.

Localized & no statistically significant 

increase. From 1972-2010 3 red 

tide/low DO fish kill events were 

reported (all red tide), as well as others 

from cold weather & unknown causes. 

Localized and no statistically significant 

increase. From 1972-2010, 3 red 

tide/low DO fish kill events were 

reported (2 red tide & 1 DO), as well as 

others from Hurricane Charlie, cold 

weather & unknown causes. 

Localized & no statistically significant 

increase. From 1972-2010 17 red 

tide/low DO related fish kill events 

were reported (8 red tide & 9 DO), as 

well as others from Hurricane Charlie, 

cold weather & unknonwn causes. Fish 

with parasites found on the west wall 

in 2009

Localized & not statistically significant 

increase. From 1972-2010 12 red 

tide/low Do fish kill events were 

reported (10 red tide & 2 DO), as well 

as others from Hurricane Charlie, cold 

weather & unknown causes. In 2002 

and 2003 fish with lesions were 

reported. 

Localized & no statistically significant 

increase. From 1972-2010 6 red 

tide/low DO fish kill events were 

reported (1 red tide & 5 DO), as well as 

others from cold weather & unknown 

causes. Caloosahatchee River shows 

history of fish kills related to disease 

and lesions. 

Localized & no statistically significant 

increase. From 1972-2010 11 red 

tide/low DO fish kill events were 

reported (9 red tide & 2 low DO), as 

well as others from cold weather & 

unknow sources. Also, 2008 fish kill 

related to lesions. 

Source FWC Fish Kill Hotline Data. Personal Observation. FWC Fish Kill 

Hotline Data.

FWC Fish Kill Hotline Data. Personal Observation. FWC Fish Kill 

Hotline Data.

Personal Observation. FWC Fish Kill 

Hotline Data.

Personal Observation. FWC Fish Kill 

Hotline Data.

Personal Observation. FWC Fish Kill 

Hotline Data.

FWC Fish Kill Hotline Data.

Fish kills:

Coral/hardbottom community changes or loss:

Impacts to benthic community:
Nutrient Factors Dona & Roberts Bays Lemon Bay Myakka River Peace River Charlotte Harbor & Cape Haze Pine Island Sound & Matlacha Pass

Tidal Caloosahatche River & San Carlos 

Bay Estero Bay

Observed? No No No No No No No No

Explanation Comparisons between 1990 and 2005 

analysis show decreases. CHNEP 

Management Conference will evaluate 

comparisons by end of 2010.

Comparisons between 1990 and 2005 

analysis show decreases. CHNEP 

Management Conference will evaluate 

comparisons by end of 2010.

Comparisons between 1990 and 2005 analysis 

show decreases. CHNEP Management 

Conference will evaluate comparisons by end of 

2010.

Comparisons between 1990 and 2005 

analysis show decreases. CHNEP 

Management Conference will evaluate 

comparisons by end of 2010.

Comparisons between 1990 and 2005 

analysis show decreases. CHNEP 

Management Conference will evaluate 

comparisons by end of 2010.

Comparisons between 1990 and 2005 

analysis show decreases. CHNEP 

Management Conference will evaluate 

comparisons by end of 2010.

Comparisons between 1990 and 2005 

analysis show decreases. CHNEP 

Management Conference will evaluate 

comparisons by end of 2010.

Comparisons between 1990 and 2005 

analysis show decreases. CHNEP 

Management Conference will evaluate 

comparisons by end of 2010.

Source Synthesis of Existing Information 1999. 

CHNEP/Janicki Pollutant Loading 

Technical Report, 2010. 

Synthesis of Existing Information 1999. 

CHNEP/Janicki Pollutant Loading 

Technical Report, 2010. 

Synthesis of Existing Information 1999. 

CHNEP/Janicki Pollutant Loading Technical 

Report, 2010. 

Synthesis of Existing Information 1999. 

CHNEP/Janicki Pollutant Loading 

Technical Report, 2010. 

Synthesis of Existing Information 1999. 

CHNEP/Janicki Pollutant Loading 

Technical Report, 2010. 

Synthesis of Existing Information 1999. 

CHNEP/Janicki Pollutant Loading 

Technical Report, 2010. 

Synthesis of Existing Information 1999. 

CHNEP/Janicki Pollutant Loading 

Technical Report, 2010. 

Synthesis of Existing Information 1999. 

CHNEP/Janicki Pollutant Loading 

Technical Report, 2010. 

Observed? Unlikely Possibly Yes Yes Yes Possibly Possibly Yes

Explanation Not impaired for Chlorophyll a. 

Decreasing trends for total nitrogen and 

increasing total phosphorous trends.

Not impaired for Chlorophyll a. Upper 

Lemon Bay shows increasing trends for 

ammonia. Decreasing nitrate+nitrite 

and total nitorgen trends. Mixed trends 

for total phophorous.

Impaired for Chlorophyll a. Increasing 

chlorophyll a, ammonia, and total nitrogen 

trends. Decreasing total phosphorous trends

Impaired for Chlorophyll a. No trends 

for chlorophyll a, ammonia, total 

nitrogen, . Decreasing trends for 

nitrate+nitrite, Increasing trend for 

orthophosphate and total phosphorous.

Upper Charlotte Harbor impaired for 

Chlorophyll a. No Chlorophyll a trends. 

Increasing trend of orthophosphate and 

total nitrogen off of Bokeelia.

Not impaired for Chlorophyll a. 

Improving trends for chlorophyll a and 

orthophosphate in Pine Isalnd Sound. 

Increasing trend of orthophosphate in 

Matlacha pass. Increasing trend of total 

nirtogen

Not impaired for Chlorophyll a. San 

Carlos Bay has no Chlorophyll a and 

orthophosphate trends Increaing trend 

for nitrate+ nitrite, total nitrogen

Estero Bay not listed as impaired for 

Chlorophyll a. Some tidal tributaries are 

listed as impaired. No Chlorophyll a and 

orthophosphate trends. Several stations 

have increasing trend for ammonia, 

total nitrogen. Some stations show 

decreasing trend for total phosphorous.

Source CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki Water 

Quality Data Analysis & Report for CHNEP, 2007.

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

CHNEP Maps of FDEP 303(d) listing of 

impairments, 2010. CHNEP/Janicki 

Water Quality Data Analysis & Report 

for CHNEP, 2007.

Observed? Unknown at this time. Unknown at this time. Unknown at this time. Unknown at this time. Unknown at this time. Unknown at this time. Unknown at this time. Unsknown at this time.

Explanation

Source

Observed? Yes Yes Yes Yes Yes Yes Yes Yes

Explanation Color Dissolved Organic Matter (CDOM) 

is a confounding factor in determining 

relationships between nutrients and 

chlorophyll levels. CDOM dampens 

expression of chlorophyll.

Color Dissolved Organic Matter (CDOM) 

is a confounding factor in determining 

relationships between nutrients and 

chlorophyll levels. CDOM dampens 

expression of chlorophyll.

Color Dissolved Organic Matter (CDOM) is a 

confounding factor in determining relationships 

between nutrients and chlorophyll levels. CDOM 

dampens expression of chlorophyll.

Color Dissolved Organic Matter (CDOM) 

is a confounding factor in determining 

relationships between nutrients and 

chlorophyll levels. CDOM dampens 

expression of chlorophyll.

Color Dissolved Organic Matter (CDOM) 

is a confounding factor in determining 

relationships between nutrients and 

chlorophyll levels. CDOM dampens 

expression of chlorophyll.

Color Dissolved Organic Matter (CDOM) 

is a confounding factor in determining 

relationships between nutrients and 

chlorophyll levels. CDOM dampens 

expression of chlorophyll.

Color Dissolved Organic Matter (CDOM) 

is a confounding factor in determining 

relationships between nutrients and 

chlorophyll levels. CDOM dampens 

expression of chlorophyll.

Color Dissolved Organic Matter (CDOM) 

is a confounding factor in determining 

relationships between nutrients and 

chlorophyll levels. CDOM dampens 

expression of chlorophyll.

Source Tomasko, 2008. Analysis of clear lakes 

and lakes with color.

Tomasko, 2008. Analysis of clear lakes 

and lakes with color.

Tomasko, 2008. Analysis of clear lakes and lakes 

with color.

Tomasko, 2008. Analysis of clear lakes 

and lakes with color.

Tomasko, 2008. Analysis of clear lakes 

and lakes with color.

Tomasko, 2008. Analysis of clear lakes 

and lakes with color.

Tomasko, 2008. Analysis of clear lakes 

and lakes with color.

Tomasko, 2008. Analysis of clear lakes 

and lakes with color.

Observed? Yes Yes Yes Yes Yes Yes Yes Yes

Explanation Localized. Construction of ICW & 

"hardening" of shorelines.

Localized. Construction of ICW & bridge 

causeways & "hardening" of shoreline.

Localized. Construction residential canals & 

"hardening" of shoreline.

Localized. Construction residential 

canals & "hardening" of shoreline.

Localized. Construction of residential 

canals, water control structures on 

Coral Creek & "hardening" of 

shorelines.

Construction of ICW, Sanibel Causeway, 

residential canals, water control 

structures on Caloosahatchee R & 

"hardening" of shorelines.

Connection to Lake Okeechobee and 

Kissimmee basin coupled with 

construction of S-79 barrier which 

alternatively expand and contract the 

watershed, dramatically affecting 

hydrology. Construction of ICW, Sanibel 

Causeway, residential canals & 

"hardening" of shorelines.

Construction water control structures 

on Caloosahatchee R & "hardening" of 

shorelines.

Source --- --- --- --- --- --- --- ---

Observed? Unknown at this time. Unknown at this time. Yes Yes Yes Yes Yes Unknown at this time.

Explanation Hurricane Charlie 2004. Hurricane Charlie 2004. Hurricane Charlie 2004. Hurricane Charlie 2004. Hurricane Charlie 2004.

Source --- --- --- --- ---

Natural high-nutrient episodes (e.g., seasonal or event driven):

Table 1b. Checklist of additional factors for each estuary within the CHNEP watershed. 

CHNEP Estuary Segment

Increased nutrient loading:

Difference between nearshore & offshore levels:

Mitigating factors that could prevent nutrient expression:

Other significant stressors to biological communitors:

Increased nutrient concentrations: