4 

Long-term trends in the water quality of Florida Bay (1989 - 2000) 

Joseph N. Boyer & Ronald D. Jones 

Southeast Environmental Research Center, Florida International University, Miami, FL 33199 

 One of the primary purposes for conducting long-term monitoring projects is to be able to 

detect trends in the measured variables over time. These programs are usually initiated as a 

response to public perception (and possibly some scientific data) that 'the river-bay-prairie-forestetc. is dying'. In the case of Florida Bay during 1987, the impetus was the combination of a 

seagrass die-off, increased phytoplankton abundance, sponge mortality, and a perceived decline 

in fisheries. In response to these phenomena, a network of water quality monitoring stations was 

established in 1989 to explicate both spatial patterns and temporal trends in water quality in an 

effort to elucidate mechanisms behind the recent ecological change. 

Overall Period of Record

 A spatial analysis of data from our monitoring program resulted in the delineation of 3 groups 

of stations which have robust similarities in water quality (Fig. 1). We have argued that these 

spatially contiguous groups of stations are the result of similar loading and processing of 

materials, hence we call them 'zones of similar influence'. The Eastern Bay zone acts most like a 

'conventional' estuary in that it has a quasi-longitudinal salinity gradient caused by the mixing of 

freshwater runoff with seawater. In contrast, the Central Bay is a hydrographically isolated area 

with low and infrequent terrestrial freshwater input, a long water residence time, and high 

evaporative potential. The Western Bay zone is the most influenced by the Gulf of Mexico tides 

and is also isolated from direct overland freshwater sources. 

 Climactic changes occurring over the data collection period of record had major effects on 

the health of the bay. Precipitation rebounded from the drought during the late 80's being greater 

than the long term average (9.2 cm mo-1) for the last 7 of 10 years (Fig 2.). Over this period, 

salinity and total phosphorus (TP) concentrations declined baywide while turbidity (cloudiness of 

the water) increased dramatically. The salinity decline in Eastern, Central and Western Florida 

Bay was 13.6, 11.6, and 5.6 psu, respectively (Fig. 3). Some of this decrease in Eastern Bay 

could be accounted for by increased freshwater flows from the Everglades but declines in other 

areas point to the climactic effect of increased rainfall during this period. The Central Bay 

continues to experience hypersaline conditions (>35 psu) during the summer but the extent and 

duration of the events is much smaller. 

 As mentioned previously, TP concentrations have declined baywide over the 10 year period 

(Fig. 4). The Eastern Bay has the lowest concentrations while the Central Bay is highest. Unlike 

most other estuaries, increased terrestrial runoff may have been partially responsible for the 

decrease in TP concentrations in the Eastern Bay. This is because the TP concentrations of the 

runoff are at or below ambient levels in the bay. The elevated TP in the Central Bay is mostly 

due to concentration effect of high evaporation. It is important to understand that almost all the 

phosphorus measured as TP is in the form of organic matter which is less accessible to plants and 

algae than inorganic phosphate. 

 Turbidity in Eastern Bay increased 2-fold from 1991-98, while Central and Western Bays 

increased by factors of 20 and 4, respectively (Fig. 5). Generally, the Eastern Bay has the clearest 
 

 5 

water which is due to a combination of factors such as high seagrass cover, more protected 

basins, low tidal energy, and shallow sediment coverage. Turbidity in the Central and Western 

Bays have increased tremendously since 1991. We are unsure as to the cause but the loss of 

seagrass coverage may have destabilized the bottom so that it is more easily disturbed by wind 

events. 

 Chlorophyll a concentrations (Chl a), a proxy for phytoplankton biomass, were particularly 

dynamic and spatially heterogeneous (Fig. 6). In the Eastern Bay, which makes up roughly half 

of the surface area of Florida Bay, Chl a declined by 0.9 μg l-1 or 63%. The isolated Central Bay 

zone underwent a 5-fold increase in Chl a from 1989-94, then rapidly declined to previous levels 

by 1996. In Western Florida Bay, there was a significant increase in chlorophyll a, yet median 

concentrations of chlorophyll a in the water column remained modest (~2 μg l-1) by most 

estuarine standards. There were significant blooms in Central and Western Bays immediately 

following Hurricanes Georges (Nov. 1998) and Irene (Oct. 1999). It is important to note that 

these changes in turbidity and chlorophyll a happened after the poorly-understood seagrass dieoff in 1987. It is likely that the death and decomposition of large amounts of seagrass biomass 

can at least partially explain some of the changes in water quality of Florida Bay but the 

connections are temporally disjoint and the processes indirect and not well understood. 

 Ammonium (NH4

+

) levels displayed large variability over the period of record and was much 

higher in the Central Bay than anywhere else (Fig. 7). Only in Central Bay did the NH4

+

 pool 

increase substantially over time (3-6 fold). Trends in nitrate (NO3

-2) concentrations mirrored 

those of NH4

+

 and were mostly due to the biological conversion of NH4

+

 to NO3

-2 via 

nitrification (Fig. 8). Total organic carbon concentrations (TOC) vary widely among the 

different zones and show significant intra-annual cycles (Fig. 9). Highest TOC levels generally 

occur in the Central Bay during summer as a result of evaporative concentration and restricted 

mixing with the rest of the Bay. 

2000 Alone

Most water quality variables during 2000 generally followed typical annual trends but there were 

a couple exceptions. Both Central and Western Bays experienced hypersalinity during the 

summer months. Salinity in the Western Bay was ~ 45 psu during Sept.; the Central Bay got up 

to 48 psu and remained hypersaline during June – Sept. In addition, a moderate phytoplankton 

bloom (4-12 μg l-1) occurred in Central Bay during March and April. 

ACKNOWLEDGMENTS

 We thank all the field and laboratory technicians involved with this ongoing project 

especially Pete Lorenzo. This project was possible due to the continued funding of the South 

Florida Water Management District through the Everglades National Park (SFWMD/NPS 

Cooperative Agreement C-7919 and NPS/SERC Cooperative Agreement 5280-2-9017). 

 This report is contribution #TXXX of the Southeast Environmental Research Center at 

Florida International University. 

Maps of South Florida Water Quality Monitoring Network 

http://serc.fiu.edu/wqmnetwork
 

 6 

 Figure 1. Zones of similar water quality in Florida Bay 

Monthly Average Rainfall 

 Figure 2. Monthly average rainfall in the Florida Bay area. 

0

10

20

30

40

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000

cm mo -1
 

 7 

Median Salinity 

Figure 3. Monthly median salinity in the three Florida Bay zones. 

Eastern

0

10

20

30

40

50

60

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

psu 

Central

10

20

30

40

50

60

70

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

psu

W estern

25

30

35

40

45

50

55

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

psu
 

 8 

Median Total Phosphorus 

Figure 4. Monthly median total phosphorus concentration in the three Florida Bay zones. 

Eastern

0.000

0.005

0.010

0.015

0.020

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

ppm

Central

0.00

0.01

0.02

0.03

0.04

0.05

0.06

0.07

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

ppm

W estern

0.00

0.01

0.02

0.03

0.04

0.05

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

ppm
 

 9 

Median Turbidity 

Figure 5. Monthly median turbidity levels in the three Florida Bay zones. 

Eastern

0

2

4

6

8

10

12

14

16

18

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

NTU

Central

0

10

20

30

40

50

60

70

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

NTU

W estern

0

10

20

30

40

50

60

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

NTU
 

 10 

Median Chlorophyll a

Figure 6. Monthly median chlorophyll a concentrations in the three Florida Bay zones. 

Eastern

0.0

0.5

1.0

1.5

2.0

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

μg l-1

Central

0

5

10

15

20

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

μg l-1

W estern

0

2

4

6

8

10

12

14

16

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

μg l-1
 

 11 

Median Ammonium (NH4

+

) 

Figure 7. Monthly median ammonium concentrations in the three Florida Bay zones. 

Eastern

0.00

0.02

0.04

0.06

0.08

0.10

0.12

0.14

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

ppm

Central

0.0

0.1

0.2

0.3

0.4

0.5

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

ppm

W estern

0.00

0.02

0.04

0.06

0.08

0.10

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

ppm
 

 12 

Median Nitrate (NO3

-2) 

Figure 8. Monthly median nitrate concentrations in the three Florida Bay zones. 

Eastern

0.00

0.01

0.02

0.03

0.04

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

ppm

Central

0.00

0.01

0.02

0.03

0.04

0.05

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

ppm

W estern

0.00

0.01

0.02

0.03

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

ppm
 

 13 

Median Total Organic Carbon (TOC) 

Figure 9. Monthly median TOC concentrations in the three Florida Bay zones. 

Eastern

4

6

8

10

12

14

16

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

ppm

Central

0

5

10

15

20

25

30

35

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

ppm

W estern

0

2

4

6

8

10

12

14

1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001

ppm