2016 Pensacola Bay Area Water Quality Report

The Florida Sea Grant Program in Escambia County provides this service each year. The purpose is to provide the general public with data and information about the state of the water quality in our area. Historically our bay has suffered much and, in terms of sediments, is considered one of the more polluted bays in the state. However, the water column itself is not as bad and has improved significantly over the years. Large fish kills common in the 1960’s and ‘70’s are no longer common, in fact rare.


Fish Kills

Fish kills can be caused by many factors. The large kills of a few decades ago were more often than not triggered by hypoxia, or a depletion of dissolved oxygen in the water. DO concentrations below 4.0 ppm have been problematic for some species, and below 3.0 problematic for most species.

Hypoxia can be triggered by warm water temperatures and high rates of biological demand (decomposition). Warm temperatures, of course, come in the summer and are out of our control. Decomposition can be increased with increased organics entering the system. Sewage (both human and animal), leaf litter, discarded remains from cleaning fish are just some of the examples of organics that can cause this problem. Humans contribute a lot of these organics and simple behavioral changes can help reduce them.

Another cause of hypoxia is a process called eutrophication. This process is caused by excessive nutrients in the water column. Excessive nutrients can lead to a bloom of microscopic plants which will darken the water column, blocking needed light to seagrasses. Eventually these phytoplankton die and settle on the bottom, where they decompose contributing to the organic problem mentioned earlier. Water bodies with high levels of nutrients are termed eutrophic. Many lakes and bayous in the state are naturally high in nutrients but others have become this way with our development around them. Hypereutrophic is the term used for water bodies that have excessive nutrients within them. The cause of excessive nutrients can be sewage (both human and animal) and fertilizers used on our lawns. Again, some simple behavior changes can help reduce this problem.


Below is the rubric used by the UF/IFAS LAKEWATCH program for selected measured parameters used by volunteers.

UF/IFAS LAKEWATCH rubric for nutrient scoring

Category Oligotrophic Mesotrophic


Total Phosphorus


< 15 15 – 25 25 – 100 > 100
Total Nitrogen


< 400 400 – 600 600 – 1000 > 1000
Chlorophyll a


< 0.5 0.5 – 1.8 1.8 – 12.4 > 12.4


> 13.1 13.1 – 8.2 8.2 – 3.2 < 3.2


Health Advisories

Health advisories are issued for bodies of water where indicator bacteria levels are too high and could be a public health risk. Currently water quality monitors measure for Enterococcus bacteria in salt water systems. Enterococcus bacteria are found in the digestive tracts of birds and mammals and aid in digestion. They are harmless to us but serve as an indicator that excessive amounts of sewage are in the water and other pathogenic bacteria could be present. The Florida Department of Environmental Protection uses the value of 104 colonies as the high point. If there are more than 104 colonies/100ml of sample, a second sample will be analyzed to confirm. If this sample is also high a health advisory will be issued. High levels of bacteria are associated with heavy rainfall – suggesting a connection with stormwater run-off. There is also the leaching of septic tank discharges from the sand on the property to the nearby waterways.


Sampling and Analysis Quality

It is important that the sampling and analysis of those samples, be conducted under a standard that assures quality control.


LAKEWATCH – The UF/IFAS LAKEWATCH program has been approved by the state DEP. Studies have shown no significant difference in samples collected and analyzed by certified state labs and those by UF/IFAS LAKEWATCH volunteers for the same bodies of water. All LAKEWATCH volunteers are trained to use UF/IFAS LAKEWATCH protocols.


FLORIDA DEPARTMENT OF ENVIRONMENTAL PROTECTION – samples and analyzes their stations using state certified technicians.


FLORIDA FISH AND WILDLIFE CONSERVATION COMMISSION – houses statewide fish kill data. Fish can be reported (and viewed) on their website.


ESCAMBIA COUNTY MARINE SCIENCE PROGRAMS – are not state certified. The water quality protocols being used by these marine science students are those presented to the teachers by environmental scientists at the University of West Florida. These protocols are strictly adhered to. The Diversity and Abudance study is using the Shannon Index, a preferred index used by certified field biologists. Fish identification is confirmed by the Florida Sea Grant Agent.


MICROPLASTICS – the protocols for the microplastics sampling and analysis were developed by Dr. Maia McGuire at Florida Sea Grant. Dr. McGuire worked with other microplastic monitoring programs from around the country to develop these protocols. Each volunteer is trained how to sample and analyze.


Bayou Texar


No LAKEWATCH data for Bayou Texar this year was available.


FDEP and Health Advisories

Year # of samples # of health advisories %of samples advisory issued Highest Count Mean

2012 13 3 .21 600 92

2013 21 2 .10 600 46

2014 43 8 .19 700 78

2015 38 9 .24 1390 158

2016 25 4 .16 192 39

Total 140 26 .18

Bayou Texar is a location that is monitored on a routine basis. There was an increase in health advisories during 2014 and 2015 but there was also an increase in monitoring. However, the percent of samples that caused an advisory have remained around 20%.


FWC and Fish Kills

2012 100 dead menhaden in May; could be hypoxia

2013 no fish kills reported

2014 40 dead menhaden in September; 300 menhaden in October; could be hypoxia

2015 no fish kills reported

2016 no fish kills reported

mean = 0.6 fish kills / year – 147 fish / kill

Menhaden are a species with low tolerance to low DO levels. Kills involving many of this fish indicate possible hypoxia.

Escambia Marine Science Educators Monitoring

The Marine Science Academy at Washington High School has been monitoring 4 stations on Bayou Texar since 2013. The Academy students monitor water temperature, salinity, dissolved oxygen, total nitrogen, total phosphorus, chlorophyll a, and pH. All measurements are from the shoreline and not in the deep sections of the bayou.

The values posted below are the MEAN values for the year for each station

Station 1 12th Avenue Bridge

Station 2 Hyde Park Road access

Station 3 Public boat ramp near Cervantes (eastside of the Bayou)

Station 4 Bayview Park

Station 1 Temp (C)


Salinity (‰) DO (ppm) TN (µg/L) TP (µg/L) Chlorophyll


2013 21.8 0.4 4.4 1150 26.7 10.8
2014 19.8 0.2 5.4 855.5 90.0 3.4
2015 21.3 1.5 5.4 954.7 379.2 5.1
2016 21.1 0.1 6.2 936.7 370.9 1.5


Station 2 Temp (C)


Salinity (‰) DO (ppm) TN (µg/L) TP (µg/L) Chlorophyll


2013 24.9 9.7 7.5 1816.7 6.7 91.2
2014 22.7 10.6 8.1 441.7 34.2 27.2
2015 22.8 12.3 7.6 442.4 329.4 20.9
2016 22.1 2.5 8.0 495.0 469.2 7.4

Station 3 Temp (C)


Salinity (‰) DO (ppm) TN (µg/L) TP (µg/L) Chlorophyll


2013 23.8 12.3 8.1 633.3 8.3 63.6
2014 21.1 11.7 8.2 325.0 37.5 13.9
2015 21.8 14.0 7.3 367.1 528.2 18.0
2016 20.9 8.3 8.0 420.8 476.7 5.5

Station 4 Temp (C)


Salinity (‰) DO (ppm) TN (µg/L) TP (µg/L) Chlorophyll


2013 23.8 13.0 7.8 500.0 10.0 61.0
2014 21.9 10.1 8.2 275.0 38.3 19.5
2015 22.2 13.7 7.7 398.3 423.5 14.0
2016 21.9 4.0 8.2 450.0 483.3 6.4


Temperature: consistent over time; 20-22 C

Salinity: was significantly higher at Station 1 (2015); significantly lower at stations 2-4 (2016); Probably due to rainfall amounts

Dissolved oxygen: lower at station 1 than rest of the bayou

Total Nitrogen: hypereutrophic at station 2 (2013); levels of chlorophyll were also hypereutrophic;

nitrogen very low at stations 3 and 4 (2014, 2015). Total nitrogen has decreased over

time at stations 2-4.

Total Phosphorus: the levels have increased significantly in 2015 and 2016 at all stations. This is

also the time when construction on the new 12th Avenue Bridge began.

Chlorophyll: concentrations were very high, hypereutrophic, in 2013. There has been a consistent

decline in concentration of chlorophyll over time.

Bayou Chico


LAKEWATCH volunteers collect from three locations in their assigned water body every other month. Sampling includes secchi reading (this is using a white disk to determine water clarity), total nitrogen, total phosphorus, and total chlorophyll – all of which are indicators of nutrient issues.



There were high levels of chlorophyll upper portion of Bayou Chico, where the “Y” meets. Chlorophyll is an indicator of high nutrients and low amount of submerged grasses. High chlorophyll COULD trigger low dissolved oxygen and possibly fish kills. See DEP data below. Based on this data, Chico scored as Eutrophic 62% of the time, Hypereutrophic 19% of the time and all of the hypereutrophic scores came from Stations 1-2 (upper end of the bayou).


The secchi readings near the mouth of the bayou were hypereutrophic but the nutrients and chlorophyll were not. This suggests not nutrients but sediments causing the turbidity of the water to be high. The data also suggest that the high nutrient value was a “spike” in the graph- not consistent with other values; this suggests that there was a run-off event (or two) that caused this – probably heavy rain day(s) that increased sediments in the water. Eutrophic scores occurred 36% of the time, as did the Mesotrophic scores (36%); Hypereutrophic occurred only 6% of the time. Oligotrophic scores occurred 22% of the time; up 175%. This suggests that there were fewer problems with nutrients in 2015; maybe because of fewer rain events – not sure.


FDEP and Health Advisories

Year # of samples # of health advisories %of samples advisory issued Highest Count Mean

2012 8 4 .50 600 241

2013 10 3 .30 310 87

2014 18 7 .39 1530 185

2015 14 5 .36 1220 291

2016 12 3 .25 570 97

Total 62 27 .44

The frequency of sampling in Bayou Chico has declined. This is primarily due to budget cuts. Of the samples taken, the percentage of those where an advisory was issued as declined. One must be careful with conclusions from this – more sampling is needed. We are looking into a program where volunteers can help with this problem.


FWC and Fish Kills

2012 1 fish kill reported; 70 dead fish in August

2013 no fish kills reported

2014 2 fish kills reported; both in September; 100 menhaden, 200 menhaden, could be hypoxia

2015 no fish kills reported

2016 no fish kills reported

mean = 0.6 fish kills / year – 123 fish / kill

The species listed in 2012 was not identified. Menhaden, again, could be interpreted as a hypoxic event. These events can be triggered by rain storms and/or events with high winds stirring up the bottom and bringing the low oxygenated bottom water to the surface – triggering a fish kill.

Escambia Marine Science Educators Monitoring

There are currently no EMSE monitoring Bayou Chico.


Bayou Grande


LAKEWATCH volunteers collect from three locations in their assigned water body every other month. Sampling includes secchi reading (this is using a white disk to determine water clarity), total nitrogen, total phosphorus, and total chlorophyll – all of which are indicators of nutrient issues.



These samples do not include data for chlorophyll nor secchi readings – though these data were collected; not sure what happened. 56% of the Total Nitrogen and Total Phosphorus data score as Oligotrophic; low in nutrients. 0% scored as Hypereutrophic.


Cholorphyll data was available for 2013. The cholorophyll and secchi data suggest there was an excess of nutrients in Bayou Grande in 2013. 30% were scored as Eutrophic and 21% were scored as Hypereutrophic. Chlorophyll’s were high across the bayou, the turbidity increased closer to the mouth.


Nutrients were elevated in Grande in 2014 but had reduced from 2013. 0% of the scored data were Hypereutrophic but 47% scored as Eutrophic.


FDEP and Health Advisories

Year # of samples # of health advisories %of samples advisory issued Highest Count Mean

2012 8 2 .25 350 85

2013 11 2 .18 340 54

2014 19 7 .34 900 140

2015 14 4 .28 1380 281

2016 12 2 .17 590 79

Total 64 17 .26

As with Bayou Chico, the percentage of samples where a health advisory needs to be issued has decreased, but so has sampling effort.

FWC and Fish Kills

2012 no fish kills reported

2013 no fish kills reported

2014 no fish kills reported

2015 1 abnormal fish found at boat reported

2016 no fish kills reported

mean = 0.0 fish kills / year

Only one “fish kill” was reported from Bayou Grande since 2014. That actually was not a fish kill at all but a report of an abnormal looking jack crevalle.


Escambia Marine Science Educators Monitoring

West Florida High School is monitoring one station in Bayou Grande but we do not currently have any data from their project. Escambia High School is making plans to monitor four stations but have not begun at this time.


Central Perdido Bay


LAKEWATCH volunteers collect from three locations in their assigned water body every other month. Sampling includes secchi reading (this is using a white disk to determine water clarity), total nitrogen, total phosphorus, and total chlorophyll – all of which are indicators of nutrient issues.



Not one of the samples collected at any of the three stations in central Perdido Bay scored as Hypereutrophic (0%); however, 50% of them scored as Eutrophic. The total nutrient values were low (mesotrophic – oligotrophic) but the chlorophyll and clarity values scored as eutrophic.


A repeat of 2014, the majority of the values scored as Eutrophic (44%) and there were no values scored as Hypereutrophic (0%). A few of the chlorophyll values scored as mesotrophic but the majority were still eutrophic; suggesting less nutrients in the system in 2015.



The LAKEWATCH volunteer for central Perdido Bay used a YSI to monitor dissolved oxygen in the middle of the bay this year. The volunteer was becoming comfortable with the equipment and will continue to monitor in the future. The question many have is what are the DO values at depth in the bay? Are they hypoxic? Would this discourage marine resource restoration (such as seagrasses or scallops)?


2016 DO (ppm)
Station Month Time Bottom

Temp (F°)

Depth 1 ft 5 ft 9 ft
1 May 0100 79.6   7.2 7.3 7.4
30°19 15.54 Jun 0300 84.5   7.3 7.0 5.5
87°30 9.54 Jul 0940 87.9   6.5   4.8
  Sep 1215 85.7   7.4   5.3
  Oct 1200 80.7   7.6   6.7
  Nov 1145 76.7   7.5   6.5
2 Jun 0345 85.0   7.3 6.8 6.6
30°19 12.00 Jul 1011 88.6   6.2   4.7
87°27 16.26 Sep 1240 85.8   7.1   2.9
  Sep 1100 87.9   6.3   1.1
  Oct 1305 79.4   8.6   8.6
  Nov 1130 75.4   7.5   7.1
3 May 0100 78.2   7.6 7.4 5.9
30°26 24.0 Jul 1500 88.8   7.7   2.8
87°30 9.54 Jul 1500 88.3   6.4   2.9
  Jul 1030 88.2   6.6   1.9
  Same day 1410 88.7   2.6   2.0
  Aug 1700 Nd   7.0   4.9
  Sep 1517 86.3   7.0   6.4
  Oct 1330 85.3   7.9   4.0
  Nov 1215 77.0   7.0   4.0
4 Jul 0930 86.0   6.7   5.1
30°19 25.98 Jul 1430 86.0   6.8   4.6
87°30 32.54 Jul 0920 87.8   5.9   5.4
5 Jul 1513 88.6   7.0   1.6
30°20 28.71              
87°25 23.94              
6 Jul 1600 88.3   7.1   3.7
30°21 18.73              
87°27 18.63            


Water reaches a state of hypoxia (low dissolved oxygen) when values are below 3.0 ppm. Hypoxia can be caused by a variety of reasons: warm water temperatures, lack of current, increased biological demand (breakdown of excessive decaying organic matter). Excessive decaying organic matter can be caused by excessive nutrients increasing primary productivity and eventually excessive biomass. Dying biomass can have a high dissolved oxygen demand and lower the amount of DO in the water column. Low DO can reduce the amount of marine life in the area.


FDEP and Health Advisories

Year # of samples # of health advisories %of samples advisory issued Highest Count Mean

2012 12 0 .00 24 8

2013 14 0 .00 76 13

2014 39 4 .10 570 41

2015 31 1 .03 144 19

2016 7 0 .00 40 11

Total 103 5 .05


Unlike the bayous, whose percentage of samples having to be classified as a health advisory runs between 20-40%, central Perdido Bay has had only 5% of its samples classified such over the last 5 years. Health advisories are not a large issue here. However, it is noted that if you sample more you will find more days when advisories must be issued. So frequent monitoring is still needed here.

FWC and Fish Kills

2012 2 fish kills reported; 100 mixed species in June, 3 dead fish in July

2013 1 fish kill reported; 10 dead fish in February

2014 2 fish kills reported; 300 in January, 19 in February

2015 no fish kills reported

2016 no fish kills reported

Mean = 1 kill / year – 86 fish / kill


The species were not listed in these reports so hard to say why. Many reports to FWC are “bait kills” – meaning discarded fish from cast nets, and sometimes can be in high numbers. So not sure the possible cause of these kills. However, these data do suggest more fish kill reports here than in the bayous.

Escambia Marine Science Educators Monitoring

There are currently no EMSE programs monitoring Perdido Bay and no plans to include one in the near future.



Diversity of Abundance of Nearshore Fishes in Pensacola Bay

The Marine Science Academy at Washington High School began monitoring nearshore fish diversity in 1992. The students collected small bait fish using a 50×4’ seine (1/8” mesh).


1992 – 1997

The Academy sampled Bayou Texar, Pensacola Bay, and Santa Rosa Sound

They pulled the net 3 times at each location; fish identified to species and the number of each logged. MSA also pulled a 16’ otter trawl from a 19’ Cape Horn boat. The trawl was pulled in 0-20’ of water for 30 minutes. Two trawls in the bay and two in the sound.

43,284 fish were collected; 105 species were identified

Shannon Index H = 1.63

Top 5 species:

  1. Silverside Minnow (57%)
  2. Pinfish (18%)
  3. Mullet (6%)
  4. Spot Croaker (5%)
  5. Silver Perch (3%)


The Academy sampled Bayou Texar, Pensacola Bay, and Santa Rosa Sound (not all stations were same location as 1992-1997 surveys).

They pulled the net once for 2.5 minutes at each station. They no longer pull the otter trawl.

2,166 fish were collected; 14 species identified

Shannon Index H = 0.602

Top 5 Species:

  1. Silverside Minnow (88%)
  2. Pinfish (3%)
  3. Spot Croaker (3%)
  4. Spotfin Mojarra (2%)
  5. Longnose Killifish (1%)


The methods between the two surveys are quite different. This was due to both the availability of a trawl and boat as well as permits that allowed it. MSA will continue to monitor D&A at these locations while three other marine science programs are now making plans to add this to their program. Two of these will be sampling Bayou Grande, one Escambia Bay at Floridatown.



In recent years the topic of microplastics has made the radar. Microplastics are small pieces of plastic (< 5mm) found in the marine environment. Some pieces are primary – meaning they were intentionally produced this size for a variety of products or to melt in forms to produce large products. Others are secondary – meaning they were large pieces drifting in the ocean; the sea and sun broke them down to small pieces which are still drifting. Escambia County currently has 8 volunteers monitoring 22 locations for the abundance and type of microplastics found in our area.


22 stations

6 stations are monitored on Pensacola Bay

3 stations are monitored on the Gulf of Mexico, Bayou Grande, and Santa Rosa Sound

2 stations are monitored on Escambia Bay

1 station is monitored on Bayou Texar, Thompson’s Bayou, Escambia River, the Intracoastal Waterway near Innerarity Island, and Perdido Bay.


131 samples collected


Location Number of Samples Collected
Pensacola Bay 31
Santa Rosa Sound 26
Gulf of Mexico 20
Intracoastal Waterway 10
Bayou Texar 8
Bayou Grande 7
Thompson’s Bayou 7
Escambia River 5
Perdido Bay 3


1139 Pieces of microplastic


Number of Pieces % Total Type
535 .47 Unknown – collected before we began separating type
604 .53 Known type
455 of 604 .75 Microfiber
125 of 604 .21 Microbead
24 of 604 .04 Other


Amount of Microplastic by Location


Location Total Collected Mean No. / sample % total (of 604 pieces)
Pensacola Bay 159 5 .26
Santa Rosa Sound 130 5 .22
Gulf of Mexico 80 4 .13
Escambia bay 63 5 .10
Thompson’s Bayou 57 8 .09
Bayou Texar 40 5 .07
Bayou Grande 24 3 .04
Perdido Bay 22 7 .04
Intracoastal Waterway 21 2 .03
Escambia River 8 2 .01




Nutrients and Hypoxia

The LAKEWATCH and EMSE data suggests that there is a correlation between high spikes in nutrients and rainfall events. The LAKEWATCH data shows a decrease is hypereutrophic conditions over the last year or so; again with high values during and after rain events. Neither of these volunteers are monitoring DO from the bottom of the bayous. Perdido Bay recently included this and found hypoxic levels at the bottom of central Perdido Bay during the warmer month.

This has all been understood for a while – that rainfall triggers spikes in nutrients, and benthic hypoxia occurs in the summer month. But have these triggered fish kills? Could they be a problem for seagrass, scallop, or oyster restoration?


Fish Kills

There were fish kills reported in our bayous in 2012 and 2014. Both years included large rain events and severe local flooding. In Bayou’s Texar and Chico the species reported were menhaden; this suggests hypoxia. The species in Perdido Bay were not identified and Bayou Grande did not report a fish kill during this time. The number of kills, and amount per kill, have reduced since 2014 and have reduced significantly from the 1960’s and ‘70’s.


Health Advisories

Though the sampling effort has remained relatively consistent between the bayous, the overall sampling effort for bacteria has decreased in the last two years; this is primarily due to budget cuts. The number of health advisories issued for 2016 was below the mean (for the last five years) in all four bodies of water being monitored in this project. It is also noted that the more frequent monitoring occurs, the more health advisories are issued. Sea Grant will work with Escambia County to see if we can develop a citizen volunteer sampling program for bacteria in area waters.


In 2017 Sea Grant will be providing fact sheets and programs to educate county residents on behavioral changes they can make to help reduce nutrients, sewage, and microplastics in area water ways. Please check our website – or contact the Sea Grant Agent (Rick O’Connor (850) 475-5230; roc1@ufl.edu)


Posted: December 19, 2016

Category: Coasts & Marine, Natural Resources, Water
Tags: Fish Kills, Health Advisories, Water Quality

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