Final Report 

Assessment of Plankton Resources 

and Their Environmental Interactions 

in Biscayne Bay, Florida 

[Restored and transferred to electronic form by Damon J. Gomez (NOAA/RSMAS)

in 2002 as part of the Coastal and Estuarine Data/Document Archeology and

Rescue (CEDAR) for South Florida. Sponsored by the South Florida Ecosystem

Restoration Prediction and Modeling Program. Original stored at the Library,

Rosenstiel School Marine and Atmospheric Science, University of Miami. Minor 

editorial changes were made.] 

Larry E Brand 
ACKNOWLEDGEMENTS 

This study constitutes an integral part of the Biscayne Bay 

Restoration and Enhancement Program. It is the primary goal of 

the Program to maintain, restore or enhance those qualities of 

Biscayne Bay that provide the basic character and value of the 

resource. One of the objectives set forth to effect the 

realization of this goal includes the completion of specific 

baseline studies. 

Funding for this project has been provided by the State of 

Florida through the Department of Environmental Regulation. 

Local administration of the funds has been conducted by the Dade 

County Department of Environmental Resources Management. 

The field collection and laboratory measurements were made 

with the help of Mark Gottfried, Carlos Baylon, Nidia Rodriguez 

and Vera Trainer. Additional water quality data were made 

available by Dade County Department of Environmental Resources 

Management personnel. 
TABLE OF CONTENTS 

INTRODUCTION 1 

METHODS 3 

Sampling 3 

Phytoplankton biomass and size distribution 4 

Phytoplankton community composition 5 

Photosynthetic capacity 5 

Primary productivity 6 

Nutrient bioassays 7 

Zooplankton biomass 7 

RESULTS 9 

Temperature 9 

Salinity 10 

Phytoplankton biomass 11 

Photosynthetic capacity 16 

Primary productivity 17 

Nutrient bioassays 18 

Phytoplankton abundance 19 

Zooplankton biomass and abundance 21 

CONCLUSIONS 26 

Eutrophication 26 

Productivity and food chains 27 

Turbidity 31 

Recommendations for future monitoring and study 31 

REFERENCES 34 

TABLES 38 

FIGURES 79 
INTRODUCTION 

Biscayne Bay is a rather unique environment in the United 

States, a subtropical lagoon next to a large metropolis. 

Biologically, it provides a habitat to both temperate and 

tropical species, to estuarine, coastal and even occasional 

oceanic species. This unique and diverse community provides an 

important resource for both recreational and commercial 

fisheries. Being situated next to Miami, however, the Biscayne 

Bay ecosystem has been affected by substantial anthropogenic 

impacts during the twentieth century. The recent history of 

Biscayne Bay and documentation of its environmental 

deterioration has been given in detail by Chardon (1976), Michel 

(1976), Wanless (1976) and Thorhaug et al. (1976) and need not 

be repeated here. Public officials have recognized the 

importance of Biscayne Bay to the people of the region and are 

attempting to manage this ecosystem and the human impacts upon 

it in a rational manner. A better knowledge and understanding 

of the phytoplankton and zooplankton (the base of the food 

chain) of Biscayne Bay should aid in developing rational 

management plans for the bay. 

Surprisingly little is known about the plankton of Biscayne 

Bay. A few studies (Reeve 1964, 1970, 1975; Roman, et al., 

1983) have examined the zooplankton, but apparently no one has 

examined the phytoplankton community in detail. Reported here 

is a comprehensive study, both qualitative and quantitative, of 

the phytoplankton and zooplankton of Biscayne Bay, their spatial 
and seasonal distribution, and their role in the overall 

ecosystem of the bay. This study examined not only the 

planktonic plants and animals that serve as food for the animals 

of recreational and commercial value, but also the larval stages 

of the shrimp, crabs, and fish of importance. The abundance of 

these larval stages is critically important to the abundance of 

the adult populations on the bottom or in the water column 

(Levinton, 1982). 
METHODS 

Plankton resources of the bay were assessed at 24 stations 

distributed throughout the bay (Figure 1), covering the entire 

range of environmental conditions found in Biscayne Bay. The 

correspondence between these stations and those used by DERM is 

shown in Table 1. These samples were taken monthly for a year 

(from March 1986 to February 1987) to cover the entire seasonal 

range experienced in the bay. The standing stock biomass of 

both phytoplankton and zooplankton were measured. Community 

composition was assessed using size fractionation and 

identification of the major phylogenetic groups. Primary 

productivity and photosynthetic capacity of the water column 

plankton was measured and experiments were conducted to 

determine which nutrients are in excess in the bay and which are 

potentially limiting to the plankton community. 

Samplinq 

The sampling plan was designed to cover the entire seasonal 

cycle and sample the variety of habitats and basins found 

throughout the geographic range of Biscayne Bay. 

Once a month, 12 samples were taken in north Biscayne Bay, 

and on another day (usually the following day), 12 samples were 

taken in south Biscayne Bay. At each station, 4 liters of water 

were collected by submerging 4 liter bottles one half meter 

below the surface. One half meter diameter 280 micron and 5 

inch diameter 64 micron mesh zooplankton nets were towed at 2 

knots for 5 minutes and the cod ends emptied into 1 liter and 
100 ml polyethylene jars, respectively. All samples were kept 

in large insulated chests and transported to the laboratory 

within a few hours for processing. 

Phytoplankton biomass and size distribution

Phytoplankton biomass and size distribution was measured 

monthly at all stations in Biscayne Bay. To measure total 

chlorophyll concentration, three 100 milliliter replicates of 

sample water with 1 milligram magnesium carbonate added was 

filtered onto GF/C glass fiber filters. Another 500 milliliters 

of sample water was size fractionated by first passing through 

64 micron Nitex netting, then through a 5 micron Nucleopore 

filter, and then through a GF/C glass fiber filter. The 64 

micron netting was backwashed onto a GF/C glass fiber filter. 

Each of the samples (total chlorophyll, greater than 64 micron 

fraction, 64 to 5 micron fraction, and less than 5 micron 

fraction) was extracted for 30 minutes with 10 milliliters of 

dimethyl sulfoxide in complete darkness. Then 10 milliliters of 

90% acetone was added and the extracts were stored in complete 

darkness for one hour for further chemical extraction and then 

measured in a calibrated Turner 10-000R fluorometer equipped 

with an infrared-sensitive photomultiplier. Two drops of 5% 

hydrochloric acid were added to each 20 milliliter sample, and 

after thirty seconds, fluorescence measured once again. Total 

chlorophyll, the chlorophyll size fractions, and phaeopigments 

were calculated using the equations of Parsons et al. (1984). 

The fluorometer was calibrated with pure chlorophyll. The 

methods used are derived from Parsons et al. (1984) and Burnison 

(1980). 
Phytoplankton community composition 

Samples for determination of the phytoplankton community 

composition were taken monthly at each of the 24 stations, but 

only samples from alternate months at every other station were 

analyzed to reduce expense. Unanalyzed samples were stored. 

Two 100 milliliter samples at each station were preserved, one 

with five drops' of Lugol's solution and one with 5 milliliters 

of sodium tetraborate buffered formalin. These two 

preservatives complement each other in that they preserve 

different parts of the phytoplankton community. This is 

necessary because there is no universal preservative for 

phytoplankton (Holmes et al, 1969; Guillard, 1973). Both types 

of preserved samples were placed in a settling chamber for 24 

hours and examined under a Wild inverted compound microscope. 

The major phylogenetic groups (centric diatoms, pennate diatoms, 

dinoflagellates, coccolithophores, cyanobacteria, flagellates 

and coccoids) were identified. 

Photosynthetic capacity 

The fraction of light absorbed by phytoplankton that is 

used for photosynthesis is a good indicator of general "health" 

and growth rate of the phytoplankton (Samuelsson and Oquist, 

1977; Samuelsson et al, 1978; Cullen and Renger, 1979). As 

such, it can be used in a general way to detect poor health as a 

result of such factors as pollutants, nutrient limitation and 

adverse temperatures. It was analyzed by measuring in vivo 

chlorophyll fluorescence of phytoplankton before and after the 

blockage of the photosynthetic electron transport system with 
DCMU (3-3,4-dichlorophenyl-1, 1-dimethylurea) and expressed as 

photosynthetic capacity. 

The photosynthetic capacity of the phytoplankton was 

measured monthly at 24 stations. The in vivo chlorophyll 

fluorescence of the community in three replicate samples was 

measured in a Turner 10-000R fluorometer. Then DCMU was added 

to the sample to a final concentration of 10-5 M to block the 

photosynthetic electron transport chain between photosystems I 

and II. After blockage, the DCMU enhanced chlorophyll 

fluorescence was measured and photosynthetic capacity was 

calculated according to the equations of Cullen and Renger 

(1979). 

Primary Productivity 

Primary productivity of the phytoplankton was measured by 

the 14C fixation method at every other station bimonthly. 400 

milliliter water samples were split four ways. Each 100 

milliliter sample was incubated for four hours in polycarbonate 

bottles with one microcurie Na14CO2. The four samples were 

incubated at ambient temperature at 0.3 ly/min, 0.1 ly/min, 0.03 

ly/min, and in total darkness. After four hours, the samples 

were filtered onto 0.6 micron Millipore filters. These filters 

were exposed to hydrochloric acid fumes for two minutes to 

remove inorganic calcium carbonate and then placed in 

scintillation vials with 10 milliliters of Aquasol. 

Disintegrations per minute were then counted in a liquid 

scintillation counter and the relationship between light 

intensity and photosynthetic rate determined. 
Nutrient bioassays 

In order to determine which nutrients were limiting the 

growth and biomass of phytoplankton in Biscayne Bay, one liter 

of sample water was collected in acid cleaned polycarbonate 

bottles bimonthly at every other station and prefiltered with 

200 micron mesh. This was split into 20 milliliter samples in 

polycarbonate test tubes. The potentially limiting nutrients 

considered were nitrogen, phosphorus, silicon, iron, zinc, and 

manganese. Added to three replicate test tubes were different 

nutrient combinations –- either each nutrient alone or all but 

one of the nutrients. Added to all test tubes were 10-9 M 

cobalt, 10-9 M biotin, 10-8 M vitamin B12, and 10-7 M thiamine. 

Added to some test tubes were 10-4 M nitrate, 10-5 M phosphate, 

10-4 M silicate, 10-6 M iron, 10-8 M zinc and 10-8 M manganese. 

These were incubated at ambient temperature and 0.1 ly/min. 

Growth of the phytoplankton was monitored daily by in vivo 

chlorophyll fluorescence measurements using the method of Brand 

et al. (1981). The relative importance of the different 

nutrients to the Biscayne Bay ecosystem was determined from an 

evaluation of these experiments. 

Zooplankton biomass 

Zooplankton comprise a large percentage of food used by the 

larvae of shrimp, crabs, and fish in Biscayne Bay. Their 

abundances were estimated with five minute tows with a 280 

micron mesh half meter plankton net with a flow meter nested 

inside, and with a 64 micron mesh net, taken monthly at each 

station. The large net sample was split into 4 samples. One 

sample was settled for 24 hours in a graduated centrifuge tube 
to determine wet volume of the plankton. A second sample was 

filtered onto a preweighed GF/A glass fiber filter, rinsed with 

6% ammonium formate and dried in an oven at 70 C. Ash free dry 

weight was determined by weighing the sample, ashing at 500 C 

and then weighing again (Omori and Ikeda, 1984). 

The third and fourth replicate samples from the 280 micron 

net were preserved with 5% formalin buffered with sodium 

tetraborate and 1% propylene phenoxytol in glass jars. 

Bimonthly samples from every other station were examined under a 

Wild dissecting microscope and the major phylogenetic and 

ontogenetic groups quantified. 

Microzooplankton samples from the 64 micron mesh net were 

preserved with 5% formalin buffered with sodium tetraborate. 

Bimonthly samples from every other station were placed in a 

settling chamber for 24 hours and then examined under a Wild 

inverted compound microscope for the identification of major 

groups of microzooplankton. Unanalyzed samples were stored. 
RESULTS 

In addition to presenting the data at individual stations, 

the average of the stations within types of water bodies are: I 

small northern basins (stations 1, 2, and 3), II northern canal 

mouths (stations 5, 7, and 10), III southern canal mouths 

(stations 13, 15, 20, and 21), IV northern open water (stations 

4, 6, 8, 9, 11, and 12) and V southern open water (stations 14, 

16, 17, 18, 19, 22, 23, and 24). 

Temperature 

The temperatures measured at each of the 24 stations each 

month are given in Table 2. They indicate that the entire bay 

is roughly the same temperature at any given time. Large thermal 

gradients do not exist in Biscayne Bay. The temperatures of all 

24 stations were averaged and the overall seasonal change by 

month is shown in Figure 2. In nine months out of the year 

(April to December) the bay is quite warm, ranging from 25 to 31 

degrees. In January, February and March, the temperatures were 

between 19 and 21 degrees. These wintertime temperatures are 

higher than what are normally seen in the winter in Biscayne 

Bay, based on data from 1971 to 1985 (Dr. John Wang, personal 

communication). 
Salinity 

The salinities measured at each of the stations each month 

are given in Table 3. Figure 3 shows the yearly salinity 

average for each of the open water stations (canal mouths are 

excluded) and Figure 4 shows a map of the yearly salinity 

average throughout the bay. They show that the salinity of 

northern Biscayne Bay is always a few parts per thousand lower 

than in southern Biscayne Bay. The difference is larger during 

the summer wet season than during the winter dry season, as 

illustrated in Figure 5. Figure 5 shows the average salinity of 

each of the five water body types by month. The small basins 

north of Broad Causeway (stations 1, 2 and 3) have similar 

temporal patterns (Figure 6), with Dumfoundling Bay (station 1) 

showing the strongest fluctuation. 

Canal mouths have strong fluctuations in salinity, but do 

so independently (Figures 7 and 8). This is probably the result 

of the independent opening and closing of the different canal 

locks. Therefore, rainfall data alone do not predict salinities 

at the mouths of the canals that empty into Biscayne Bay. 

Overall salinity was reasonably constant in the open waters with 

the exception of a small decline in July when the watershed 

received a particularly large amount of rainfall. The small 

northern basins and the canal mouths are more variable and also 

show an overall decline in salinity in July, August, and 

September as a result of the rainy season. 
Phytoplankton biomass 

Total chlorophyll concentrations, as a measure of 

phytoplankton biomass, at each station each month are given in 

Table 4. A map of the average yearly chlorophyll concentrations 

throughout the bay is shown in Figure 9. Chlorophyll 

concentrations are uniformly low (around 0.2 micrograms per 

liter) in the open waters in southern Biscayne Bay both 

spatially (Figure 10) and temporally (Figure 11). Open water in 

the northern bay has higher chlorophyll concentrations (Figure 

10) and shows more sporadic fluctuations. The small basins 

north of Broad Causeway (stations 1,2 and 3) generally have the 

highest average chlorophyll concentrations in the bay (Figure 

11), with Dumfoundling Bay (station 1) showing the largest 

fluctuations over time (Figure 12). Canal mouths also have 

chlorophyll concentrations higher than the open water (Figure 

11). Each canal mouth fluctuates independently of the others 

(Figures 13 and 14). An overall decline in chlorophyll 

concentrations from April to the following February is observed 

throughout the bay except for open water in the south, which has 

low phytoplankton biomass levels throughout the year (Figure 

11). The lack of a downward trend in the southern open water 

data indicates that there is not a long-term problem with the 

methods and that the overall decline is real. Two possible 

explanations seem most plausible. One is that this is part of 

the natural seasonal cycle. Note that the initial March samples 

are low in chlorophyll, similar to the concentrations observed 

in the following February. 
Thus we may be observing a spring bloom of phytoplankton in 

April and a long term decline afterward. One possible reason 

for this seasonal pattern in chlorophyll is a seasonal buildup 

and flushing of nutrients in the groundwater of Miami adjacent 

to Biscayne Bay (Dr. Brian Lapointe, personal communication). 

He has hypothesized that nutrient concentrations build up in the 

groundwater during the winter when there is very little rainfall 

and flushing. The first spring rains then flush this nutrient 

rich water into the adjacent marine waters, generating large 

phytoplankton blooms. Once the high concentrations of nutrients 

have been flushed out of the groundwater system, subsequent 

rainfalls during the summer and fall carry less nutrients into 

the local waters than the first major rainstorm of the rainy 

season. This may explain the large phytoplankton bloom in April 

when there was a significant decline in salinity as a result of 

a large amount of rainfall and the subsequent long term decline 

throughout the rest of the year. Alternatively, another 

hypothesis is that the initial March chlorophyll data are 

unusually low and we are observing part of a long-term decline 

in phytoplankton biomass in the bay. If this is the case, this 

may be evidence that the efforts to reduce nutrient inputs to 

the bay are succeeding. Unfortunately, we cannot test between 

the two hypotheses with only one year of data. 

Figures 15, 16, 17, 18 and 19 for each of the types of 

water bodies show that the higher chlorophyll concentrations are 

always associated with lower salinities. This suggests that 

runoff from land is the major source of nutrients that generate 

phytoplankton blooms in the bay. Although high chlorophyll 
concentrations are always associated with low salinity, low 

salinity water does not always have high chlorophyll 

concentrations. This indicates that freshwater runoff is 

probably the only major source of nutrients for the 

phytoplankton, but variable salinity can cause osmotic problems 

for some phytoplankton and inhibit blooms. This can be clearly 

seen in comparing the chlorophyll-salinity relationship between 

the basins north of Broad Causeway (Figure 15) and the canal 

mouths in the southern bay (Figure 17). That low salinity 

always generates high phytoplankton biomass in the basins north 

of Broad Causeway (Figure 15) is probably the result of the fact 

that salinities are persistently low in these waters and do not 

fluctuate very rapidly (Figure 6). Indigenous populations 

adapted to low salinities can be maintained in these small 

basins. On the other hand, at the canal mouths in the southern 

bay where salinity fluctuates dramatically (Figure 8), 

phytoplankton biomass never develops to high concentrations in 

salinities below 20 parts per thousand. This suggests that the 

phytoplankton in the south bay where salinities are generally 

higher are unable to adapt to the sudden drops in salinities at 

the canal mouths. 

The spatial and temporal patterns of phaeopigments, the 

degradation products of chlorophyll, are very similar to those 

seen in chlorophyll distributions. The phaeopigment 

concentrations at each station each month are given in Table 5. 

Figure 20 shows the yearly average of phaeopigment 

concentrations at each of the open water stations (canal mouths 

excluded). Phaeopigments are uniformly low in the south bay and 
increase toward the north starting near the Rickenbacker 

Causeway. Figure 21 shows the average phaeopigment 

concentrations in each type of water body by month. Virtually 

no seasonal change in phaeopigment change is observed in the 

open waters of the south bay. All other types of water bodies 

show sporadic variability (although less than observed in 

chlorophyll concentrations) and a long-term decline as was seen 

in chlorophyll concentrations. 

The ratio of chlorophyll to phaeopigments is a good 

indicator of the physiological health of phytoplankton 

populations and the grazing pressures on them. These ratios at 

each station each month are given in Table 6. Figure 22 shows 

that the ratio is consistently somewhat lower in the open waters 

of the south bay than in the north. This is most likely the 

result of stronger nutrient limitation in the south bay. The 

canal mouths and waters in the northern part of the bay have 

somewhat higher chlorophyll to phaeopigment ratios, but there is 

no obvious pattern among them (Figure 23). Figure 23 also shows 

no obvious seasonal trend in the chlorophyll to phaeopigment 

ratio. As a high chlorophyll to phaeopigments ratio indicates 

healthy, more actively growing phytoplankton, plots showing the 

generally positive relationship between the chlorophyll to 

phaeopigment ratios and total chlorophyll concentrations 

(Figures 24, 25, 26, 27 and 28) indicate that the high biomass 

and chlorophyll concentrations are the result of more active 

growth. Tables 7, 8, and 9 give the percentage of chlorophyll 

contained in particles less than 5 microns, between 5 and 60 

microns, and over 60 microns in size, respectively. Figure 29 
shows the yearly average for each of the open water stations of 

the percentages of the three size fractions of phytoplankton 

biomass measured as chlorophyll. Phytoplankton less than 5 

microns in size are dominant throughout the bay. They are about 

60% of the phytoplankton biomass in the northern part of the bay 

and around 80% in the southern part. Cells this small cannot be 

identified taxonomically without the use of an electron 

microscope. Typically, however, in marine waters the small 

cells are predominantly cyanobacteria, cryptophytes, 

eustigmatophytes, prasinophytes and prymnesiophytes. 

Phytoplankton larger than 60 microns are uniformly low 

throughout the bay, contributing about 10% of the biomass, while 

phytoplankton between 5 and 60 microns in size increase from 10% 

in the south to 30% in the north (Figure 29). Larger size 

fractions of phytoplankton also tend to be more important in the 

canal mouths (Figures 30, 31 and 32). In general, it appears 

that larger phytoplankton are more prevalent where phytoplankton 

biomass is higher and where nutrient concentrations are presumed 

to be higher. This reflects the fact that smaller phytoplankton 

are generally better adapted for low nutrient concentrations 

(Parsons and Takahashi, 1973). Smaller phytoplankton generally 

support longer food chains, resulting in much less fish 

production as a result of compounded trophic loss (Ryther, 

1969). Over the course of the year, there appears to be a small 

shift toward smaller phytoplankton (Figures 30, 31 and 32). 

This trend corresponds with the observed overall decline in 

chlorophyll throughout the year (Figure 11). 
Photosynthetic capacity 

Table 10 gives the DCMU enhanced chlorophyll fluorescence 

measured at each station each month. Figures 33, 34, 35, 36 and 

37 show the excellent relationship between DCMU enhanced 

chlorophyll fluorescence and total chlorophyll concentration 

measured by extraction. This indicates that the electron 

transport system was totally blocked by the method using DCMU 

and allows the enhanced fluorescence to be used as a good 

indicator of phytoplankton biomass. Yearly averages of the DCMU 

enhanced chlorophyll fluorescence at each of the open water 

stations (Figure 38) show the same pattern as seen earlier in 

chlorophyll concentrations, uniformly low levels in the south 

and much higher levels in the north. Figure 39 shows the 

seasonal trend in DCMU-enhanced chlorophyll fluorescence and the 

differences between the different types of water. As with 

chlorophyll, one observes an overall decline through the year 

and higher levels in canal mouths and in the north than in the 

south. 

Photosynthetic capacity is the efficiency with which solar 

energy is being channeled into the photosynthetic electron 

transport chain for the production of organic carbon and not 

being wasted as fluorescence of energy back into the 

environment. Higher photosynthetic capacity indicates more 

efficient use of solar energy. Table 11 gives the 

photosynthetic capacity measured at each station each month. 

Figure 40 shows the yearly average of photosynthetic capacity at 

each of the open water stations. Phytoplankton populations in 

the north clearly have higher photosynthetic capacities than 
those in the south, presumably as a result of more nutrients in 

the north. Figure 41 shows the seasonal change in 

photosynthetic capacity for each of the types of water bodies. 

An overall decline through the year is observed, similar to the 

decline observed in chlorophyll. As with chlorophyll, this 

decline may be attributed to a reduction in nutrient flux into 

the bay. Figures 42, 43 and 44 show that photosynthetic 

capacity tends to be lower at lower salinities. That this 

occurs in environments with higher than normal levels of 

nutrients is probably an indication of osmotic stress. 

Primary Productivity 

Rates of photosynthesis measured every other month at three 

different light intensities with phytoplankton communities from 

12 stations are shown in Table 12. Figures 45 and 46 shows the 

yearly average at the highest light intensity at each station 

and throughout the bay, indicating that planktonic primary 

productivity is about five to eight times higher in the north 

bay than in the south bay. To a large extent, this is the 

result of the much higher phytoplankton biomass in the north bay 

present to intercept the light. Figure 47 shows the seasonal 

change in maximum primary productivity in north and south bay. 

The seasonality in rates of primary productivity follows the 

seasonality in light intensity quite well, with the exception of 

somewhat higher rates in the north bay in April as a result of a 

particularly large phytoplankton bloom in the north bay at that 

time. The maximum assimilation numbers also reflect the 

seasonal change in light intensity quite well (Table 13, Figure 

4s). The assimilation number is the maximum rate of 
photosynthesis that can be carried out with a given amount of 

chlorophyll. Phytoplankton adapted to higher light intensities 

have higher rates of photosynthesis per unit chlorophyll. 

Figure 49 shows the yearly average assimilation number at each 

station. The lower assimilation numbers in the north bay are 

probably the result of more light limitation in the north bay as 

a result of more resuspended sediments and higher chlorophyll 

concentrations per liter in the north. Indeed, lower 

assimilation numbers are generally associated with higher 

chlorophyll concentrations in the north bay where chlorophyll 

concentrations are more variable (Figures 50 and 51). The 

ratios of photosynthetic rates at high and low light intensities 

can indicate the degree to which the phytoplankton are 

photoadapted to light limitation. The significantly lower 

ratios observed in the north compared to the south (Table 14, 

Figure 52) indicate that the phytoplankton in the north bay are 

indeed more adapted to light limitation. One can see the same 

photoadaptational change in the ratio on a seasonal basis in 

Figure 53. 

Nutrient bioassays 

Nutrient bioassays were conducted by both adding only one 

nutrient into each test regime and by adding all nutrients 

except one into each regime. The results are shown in Table 15. 

No obvious seasonal trends occurred, so the data were averaged 

over the entire year. Figure 54 shows the average ratio of 

growth rate with a particular added nutrient to growth rate with 

no nutrients added for each station. It clearly indicates that 

phosphorus is the primary limiting nutrient throughout the bay. 
None of the other nutrients stimulate growth very much except 

nitrogen in Dumfoundling Bay. Figure 55 shows the same ratios 

for the final biomass yield after 6 days growth with the 

different added nutrients. It also shows phosphorus to be the 

primary limiting nutrient throughout Biscayne Bay. Figure 56 

shows the average ratio of growth rate with all nutrients but 

one added to growth rate with all nutrients added. It shows not 

only that phosphorus is the primary limiting nutrient throughout 

the bay but also that nitrogen is the secondary limiting 

nutrient. Figure 57 shows the same ratios for the final biomass 

yield after 6 days growth with the different nutrients deleted. 

It also shows phosphorus and nitrogen to be the most important 

limiting nutrients. It also shows some evidence of silicon 

being partially limiting in the north bay. The overall 

conclusion of these bioassays is that phosphorus is the primary 

limiting nutrient throughout Biscayne Bay. 

Phytoplankton abundance 

Tables 16 and 17 show the abundance of the different groups 

of phytoplankton at each station throughout the year. Figures 

58 and 59 show the yearly average phytoplankton cell abundance 

at each of the stations along the central axis of the bay and 

Figure 60 shows the abundance of phytoplankton cells throughout 

Biscayne Bay. On average, phytoplankton cell concentrations are 

around five times higher in the northern bay than in the 

southern bay. Figures 61 and 62 show the average phytoplankton 

cell abundance for the northern embayments, northern open water 

and southern open water throughout the year. Although the data 

are somewhat sporadic because each preservative only preserves a 
fraction of the phytoplankton community, the data clearly show 

that phytoplankton cell abundance in the south is only around 

one fifth the abundance in the northern part of the bay. 

Furthermore, cell abundance remains uniformly low throughout the 

year in the south, and is much more variable with no clear 

seasonal trend in the north. Figures 63 and 64 show a very 

general correlation between cell abundance and chlorophyll 

concentrations in the water. The scatter reflects the variation 

in the chlorophyll content per cell in different habitats as a 

result of both cell size and photoadaptation. Figures 65 and 66 

show that chlorophyll per cell is higher in the north than in 

the south. There are two possible reasons for this trend, not 

mutually exclusive. One is that the cells are larger (Figure 

29) and thus contain more chlorophyll in the northern bay. The 

other is that the cells in the more turbid waters of the north 

bay receive less light and photoadapt (suggested by Figure 52) 

by synthesizing more chlorophyll. The possibility that 

nutritional status also influences the chlorophyll content is 

indicated by the positive chlorophyll per cell and the 

correlation between the photosynthetic capacity in the northern 

bay (Figures 67 and 68). Abundant nutrients would be expected 

to increase both cellular chlorophyll content and photosynthetic 

capacity. The trend is much less clear in the nutrient poor 

southern waters (Figures 69 and 70). 

Small coccoid cells are the dominant phytoplankton 

throughout the bay, comprising an average of around 80% of the 

phytoplankton cells in the north bay and around 90% in the south 

bay (Figures 71 and 72). Absolute concentrations of coccoid 
cells were around four or five million cells per liter in the 

north bay and one to two million per liter in the south bay 

(Figures 73 and 74). Figures 75 and 76 show no significant 

seasonal trend in the relative abundance of the coccoid cells. 

Centric diatoms comprise 10 to 20% of the phytoplankton 

community on the average in the north bay, but are 1% or less in 

the south bay (Figures 77 and 78). Figures 79 and 80 show the 

absolute concentration of centric diatoms to be far higher in 

the north bay than in the south bay. Figures 81 and 82 show a 

drop in the absolute abundance of diatoms in the open waters of 

the north bay through the year. This decline parallels the 

decline observed in the overall chlorophyll, suggesting that 

both declines may be related to a changing nutrient regime in 

the north bay. 

Pennate diatoms always comprise less than one percent of 

the phytoplankton community, with absolute abundances two to 

three times higher in the north bay than the south bay on 

average (Figures 83 and 84). 

Dinoflagellates are also always less than one percent of 

the phytoplankton community, ranging between 30 thousand and 110 

thousand cells per liter throughout the bay (Figures 85 and 86). 

Zooplankton biomass and abundance 

Table 18 shows the ash free dry weight of zooplankton at 

each station throughout the year. Figure 87 shows the yearly 

average of ash free dry weight of zooplankton at each open water 

station and Figure 88 shows the distribution throughout the bay. 

They show that zooplankton biomass is uniformly low in the south 

bay and generally two to five times higher in the north bay, 
reflecting the greater abundance of food in the north. 

Zooplankton biomass is highest in Dumfoundling Bay, where 

chlorophyll concentrations are also highest. Figure 89 shows 

the positive correlation between the yearly average 

phytoplankton biomass measured as chlorophyll and zooplankton 

biomass as ash free dry weight at each station. Table 19 shows 

the wet volume of zooplankton at each station throughout the 

year. Figure 90 shows the yearly average of zooplankton biomass 

at each open water station measured by wet volume. No obvious 

difference appears between north and south bay when zooplankton 

abundance is measured by wet volume because of the greater 

proportion of gelatinous zooplankton in the south. Figures 91 

and 92 show the seasonal change in zooplankton biomass for each 

of the different types of water bodies. They show that 

zooplankton biomass is usually higher in canal mouths than in 

open water and that zooplankton biomass is very low throughout 

the bay during summer months when water temperatures are high. 

This has been observed by others as well (Reeve, 1975). 

Tables 20 and 21 show the abundance of zooplankton groups 

at each station throughout the year sampled with the micro 

zooplankton and zooplankton nets, respectively. Figure 93, with 

yearly average abundances at each of the stations, shows that 

the tintinnids are generally about twice as abundant in north 

Biscayne Bay as in the south. Figure 94 shows that they are 

most abundant during the warm summer months when 

macrozooplankton are extremely sparse (Figures 91 and 92). In 

general the abundance of copepod nauplii (Figure 95), 

copepodites (Figure 96) and adult copepods (Figure 97) are two 
to three times higher in northern Biscayne Bay than in southern 

Biscayne Bay. All three groups were particularly high in 

Dumfoundling Bay (station 1) where food abundance is especially 

high. All developmental stages of copepods were also somewhat 

higher in Card Sound (station 24) than elsewhere in southern 

Biscayne Bay, for reasons that are not clear. Seasonality in 

the abundance of copepod nauplii, copepodites and adult copepods 

is shown in Figures 98, 99, and 100 respectively. In general, 

there appears to be an overall increase in the copepodites and 

adult copepods during the fall and winter months after a minimum 

in June. Figures 101 and 102 show that the distributions of 

shrimp larvae and juveniles are somewhat variable, although both 

are most abundant in the seagrass beds just north of the Julia 

Tuttle Causeway (station 8). Berkeley and Campos (1984) also 

found shrimp to be most abundant in the seagrass beds of the 

Julia Tuttle Causeway. This suggests that the seagrass beds in 

Biscayne Bay are important to the shrimp fishery. The juvenile 

shrimp were more abundant in the north bay than in the south. 

The shrimp larvae were generally most abundant in the fall 

(Figure 103) and the juveniles were most abundant in the winter 

(Figure 104). The abundances of ostracods (Figure 105) and 

amphipods (Figure 106) were sparse enough that their 

distributions were rather sporadic with no apparent trends 

either geographically or seasonally. Cladocerans, being 

brackish water animals, were predictably found primarily in 

Dumfoundling Bay (station 1) with very few individuals found 

elsewhere (Figure 107). Crab zoea were distributed throughout 

the bay with no obvious pattern (Figure 108), but the megalops 
stage was quite sparse with the exception of large numbers 

caught at station 19 in April (Figure 109). Polychaete larvae 

are generally around five to ten times more abundant in north 

Biscayne Bay than in the south (Figure 110), but there is no 

obvious seasonal trend. Bivalve larvae are also five to ten 

times more abundant in the north bay than in the south, but they 

are also very abundant in the middle of the bay as well (Figure 

111). Again, they are present year round with no obvious 

seasonal trend. Gastropod larvae are generally around five 

times more abundant in northern Biscayne Bay than in southern 

Biscayne Bay (Figure 112) and generally more abundant in the 

late summer and fall (Figure 113). Barnacle larvae are 

generally rather sparse, with the data dominated by large 

numbers collected at station 6 in June (Figure 114). 

Isopods are generally several times more abundant in the 

south than in the north bay (Figure 115) and most abundant in 

the spring and early summer (Figure 116). Chaetognaths were 

found throughout the bay with no obvious distributional pattern 

(Figure 117) and were most abundant in the late winter and early 

spring (Figure 118). They were least abundant during the warm 

summer months. Larvaceans were only present in any significant 

number in the spring in the extreme northern end of Biscayne Bay 

(Figures 119 and 120). Medusae were found throughout the bay 

(Figure 121) but were most prevalent in June (Figure 122). 

Fish eggs were found in high abundance only in the very 

northern part of Biscayne Bay, north of the 79th Street Causeway 

(Figure 123), but were found throughout the year (Figure 124). 
A high abundance of fish larvae was found only at Bakers 

Haulover (station 4) in April (Figure 125). 
CONCLUSIONS 

Eutrophication 

It appears fairly clear that the major source of new 

nutrients into Biscayne Bay is from land runoff through the 

canals. Large blooms of phytoplankton are observed near the 

canal mouths and phytoplankton biomass levels are higher where 

salinity is lower as a result of fresh water runoff. It does 

not appear that eutrophication has been detrimental to the food 

chain however. In fact, one finds higher abundance of animals 

in the north bay where phytoplankton abundance is higher as a 

result of eutrophication. The higher phytoplankton abundance at 

the canal mouths and in the north bay in general resulting from 

eutrophication is probably the cause of the slight depletion of 

dissolved oxygen in these areas (Alleman, 1985). Any further 

input of nutrients to the bay would reduce dissolved oxygen 

concentrations further. 

Phosphate appears to be the primary limiting nutrient in 

Biscayne Bay, probably as a result of phosphate being adsorbed 

onto the limestone of South Florida. Therefore, it is the 

addition of phosphate in runoff that contributes to 

eutrophication. The one place where nitrate is as important a 

limiting nutrient as phosphate is Dumfoundling Bay. This may be 

the result of denitrification converting much of the nitrate to 

dinitrogen gas in the anaerobic waters. The reduction of oxygen 

in Dumfoundling Bay is the result of rather stagnant water flow 
and the input of excess nutrients, resulting in the production 

of excess organic matter. Future attempts to reduce 

eutrophication of Biscayne Bay should emphasize phosphate. The 

south bay can withstand more phosphate input better than can the 

north bay because the north bay is already experiencing some 

oxygen depletion as a result of eutrophication. Channeling 

phosphate rich water through the mangroves lining the south bay 

would not only remove much of the eutrophication causing 

phosphate but also stimulate the growth of the mangroves (Onuf 

et al, 1977). 

Productivity and food chains 

Photosynthetic assimilation numbers for phytoplankton in 

Biscayne Bay are quite high (generally around 10 micrograms 

carbon/microgram chlorophyll a/hr), indicating that ultimately 

it is the low standing stock biomass of phytoplankton that 

limits planktonic productivity in the bay. These results are 

similar to the estimates of Reeve (1975). In the south bay 

where seagrasses cover 60% to 75% of the bay bottom (Markley and 

Milano, 1985) and phytoplankton are particularly sparse, 

seagrasses account for at least 80% of the total primary 

productivity. In the north bay where phytoplankton abundance is 

ten times higher and seagrasses cover only around 30% of the bay 

bottom (Markley and Milano, 1985), phytoplankton are the 

dominant primary producers and generate more organic carbon than 

seagrasses. Thus, in moving from the oligotrophic south bay to 

the eutrophic north bay, one finds a decline in seagrass 

productivity and a dramatic increase in phytoplankton 

productivity. This is associated with an increase in many types 
of animals that apparently derive more nutrition from the 

phytoplankton than from the seagrass community. Tintinnids, 

copepods, juvenile shrimp, polychaete larvae, bivalve larvae, 

gastropod larvae, larvaceans, and fish larvae are all more 

abundant in the north bay, indicating that they are probably 

more dependent on the phytoplankton for food than on the 

seagrass communities. It is generally thought that seagrass 

communities are important to many benthic animals and juvenile 

crustaceans and fish. Berkeley (1984) calculated that seagrass 

habitat supported ten times more fish by weight than a similar 

sized area that had been dredged or was barren of vegetation. 

The data presented here show that the planktonic larval stages 

are generally more abundant where phytoplankton dominate over 

seagrasses. There are several plausible reasons for this. 

First of all, very little seagrass biomass is consumed directly 

by animals. Most of the material is processed through the 

detrital food chain and is first converted to bacterial and 

fungal biomass and then to protozoan and microzooplankton 

biomass before it is available to the planktonic animals that 

feed on suspended particles. Well over 90% of the biomass is 

lost as it is processed through two additional steps in the food 

chain. As a result, planktonic animal productivity is lower in 

a seagrass community. Another reason for the higher planktonic 

animal biomass in the north bay is the greater input of 

nutrients in the north. This allows for the production of more 

animal protoplasm. In the nutrient poor south bay, productivity 

of the seagrasses is high mainly because large amounts of 

nutrient poor cellulose are being produced, not nutrient rich 
protoplasm. Thus the simple production of organic carbon is a 

poor predictor of animal production. Animal production is 

dependent on the input of nutrients and in Biscayne Bay the 

higher input of nutrients into the north bay helps contribute to 

phytoplankton dominating over the seagrasses and being the major 

primary producers of organic carbon leading to animal 

production. Seagrass beds provide important nursery areas for 

animals, but the food availability depends on the nutrient input 

to the bay. 

A rough estimate of energy flow through the planktonic food 

chain of Biscayne Bay indicates that planktonic primary 

productivity can support the fish yield of the bay. Average 

primary productivity in the bay appears to be around 40 

milligrams of carbon per square meter per day. This is in 

agreement with the findings of Roman et al. (1983). Total 

production of organic carbon by phytoplankton in the entire bay 

covering 220 square miles (Markley and Milano, 1985) would then 

be around 8.3 billion grams of carbon per year. Because most of 

the phytoplankton of Biscayne Bay are so small, they are 

probably mostly consumed by protozoa rather than copepods, 

making the food chain longer. A shift to larger phytoplankton 

that could be eaten directly by copepods would probably lead to 

about a three fold increase in the production of fish in the 

bay. Protozoa have an ecological efficiency of around 30%, 

making their yearly production around 2.5 billion grams of 

carbon. They would then be eaten primarily by copepods, which 

have an ecological efficiency of around 20%. This would lead to 

the production of around 500 million grams of carbon of copepods 
each year in Biscayne Bay. A large percentage of the fish in 

Biscayne Bay (particularly the clupeoids) can then feed directly 

on these copepods with an ecological efficiency of around 15%. 

This would lead to a yearly fish production in the bay of 75 

million grams of carbon or 750 tons of fresh weight fish. It is 

estimated that the commercial catch of fish (mostly pilchard) in 

the bay is around 80 tons each year (Berkeley, 1984). The 

recreational catch is estimated to be another 140 tons each year 

(Berkeley, 1984). It appears that the planktonic food chain 

alone could support the fish catch in Biscayne Bay, if our 

understanding of the food chain is correct. This is not to say 

that it does support the entire fishery, because undoubtedly the 

detrital food chain from the seagrasses and mangroves is 

important to many species. The estimated commercial catch of 

shrimp is 80 tons a year, with an additional 60 tons for the 

recreational catch. Adult shrimp, however, most likely depend 

more on the detrital food chain in the benthos than on the 

planktonic food chain. 

Some unknown fraction of the planktonic food chain is 

contributing to the detrital food chain and the production of 

shrimp and crabs. These fisheries do depend more directly upon 

the planktonic food chain however, because their larval stages 

feed almost exclusively upon phytoplankton and zooplankton. The 

food chain calculations show that the planktonic food chain is 

capable of supporting the fisheries in Biscayne Bay, and the 

higher abundance of animals and their larvae where phytoplankton 

are most abundant indicates that it is important. 
Turbidity 

Turbidity is a major problem in Biscayne Bay both for 

aesthetic reasons and because it reduces the amount of light 

available to seagrasses. One possible source of turbidity that 

was examined was phytoplankton blooms. Chlorophyll 

concentrations in the south bay averaged around 0.2 micrograms 

per liter and were around 2 micrograms per liter in the north 

bay. The very highest concentration of chlorophyll ever 

observed in the bay was 8.6 micrograms per liter. The data of 

Smith and Baker (1978) indicate that 0.2 micrograms chlorophyll 

per liter would allow a photic zone about 70 meters deep, 2 

micrograms per liter would allow one around 45 meters deep and 

even 8.6 micrograms per liter will allow a photic zone 10 meters 

deep. Clearly, the phytoplankton are not a major source of 

turbidity in Biscayne Bay, nor are they shading the seagrasses 

significantly. Resuspended sediments are much more important in 

reducing water clarity in Biscayne Bay. These conclusions agree 

with those of Wanless et al. (1984). 

Recommendations for future monitoring and study 

Routine monitoring of chlorophyll concentrations in the bay 

would be the best way to assess the planktonic ecosystem in 

Biscayne Bay. High concentrations of chlorophyll are a good 

indicator of the location of high inputs of nutrients to the bay 

and generally of the location of the depletion of dissolved 

oxygen in the water. Higher abundances of planktonic animals 

are also generally associated with higher chlorophyll 

concentrations. The excellent correlation between the DCMUenhanced fluorescence and the extracted chlorophyll measurements 
means that routine monitoring could be carried out quickly and 

reliably. Long term monitoring would be able to resolve several 

questions that could not be resolved in a one year study such as 

the present one. For example, the present study observed a 

rather steady decline in chlorophyll concentrations in the north 

bay over the study period of one year. Was this just the 

natural seasonal pattern of abundance in Biscayne Bay or was 

this part of a long term decline resulting from a reduction in 

nutrient inputs to the bay? Only a multiyear monitoring program 

could answer this question. A multiyear sampling program would 

also tell us how much the planktonic ecosystem of Biscayne Bay 

changes from year to year, as there probably is no "average" 

year. Such baseline data are needed before one can accurately 

identify any large scale changes resulting from anthropogenic 

perturbations. The measurement of chlorophyll concentrations 

(by DCMU enhanced fluorescence) in the bay would be the least 

expensive and most sensitive method for detecting anthropogenic 

changes. 

To document specific events that cause eutrophication in 

Biscayne Bay, detailed sampling around canal mouths should be 

made at short time intervals. Closely spaced sampling around 

canal mouths would show how far out from the canal mouths 

eutrophication is occurring and would provide an early warning 

system if the eutrophied area started to expand. The present 

sampling regime has stations too widely separated to accurately 

assess the area around canal mouths that are affected by 

eutrophication. The present sampling regime of once a month 

could only show that chlorophyll concentrations were higher when 
there was more fresh water in the canal mouth. Sampling every 

few days would allow one to determine if and when algal blooms 

develop after canal dams are opened. 
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