Characteristics of Accelerated Eutrophication in the Lower St. Johns 

River Estuary and Recommended Targets to Achieve Water Quality 

Goals for the Fulfillment of TMDL and PLRG Objectives 

John Hendrickson 

Edgar F. Lowe, Ph.D. 

Dean Dobberfuhl, Ph.D. 

Peter Sucsy, Ph.D. 

Dean Campbell

Water Resources Department Technical Memorandum No. __, 

St. Johns River Water Management District, Palatka, FL. 

August 8, 2003 
EXECUTIVE SUMMARY 

To address water and biological quality impairment of the lower St. Johns River (LSJR) 

related to excessive algal growth and accelerated eutrophication, the St. Johns River 

Water Management District and the Florida Department of Environmental Protection 

have jointly pursued the Federal Clean Water ActPs Total Maximum Daily Load (TMDL) 

process (and analogous mandates under the Florida Administrative Code Chapter 62-40 

for the determination of Pollution Load Reduction Goals (PLRG)) as a means to establish

enforceable and achievable limits on nutrient pollution. The plan to establish TMDLs

and PLRGs envisioned three large endeavors (Hendrickson and Magley, 2002): 1) an 

assessment of the external nutrient and organic carbon loads to the LSJR; 2) a series of 

diagnostic studies and monitoring designed to better describe patterns of algal community 

composition, algal productivity, nutrient utilization and sediment-water column

interactions; and 3) hydrodynamic and water quality modeling for integrating the results 

of diagnostic work and linking external nutrient loads to eutrophication effects. 

With respect to the investigations identified above, the objectives of this report are to: 

1) describe the spatial and temporal patterns in algal biomass, nutrient utilization and 

limitation, plankton community composition and water quality effects related to

eutrophication, in order to improve the general understanding of these processes, 

and to calibrate and guide revisions, if necessary, to the water quality modeling 

endeavor; and 

2) identify the point on the continuum of adverse water quality effects, stemming 

from nutrient enrichment and eutrophication, that represents significant 

impairment, for the purpose of establishing targets for water quality modeling of 

nutrient load reduction scenarios. 

St. Johns River Water Management District ii
LSJR Freshwater Reach 

The degree to which the lower St. Johns River manifests the effects of nutrient pollution 

is determined through a complex interplay of hydrodynamic, meteorologic and biological 

processes. Because of the predominant, overlapping patterns of river flow and spring ? 

summer heat and solar energy, the LSJR exhibits a strong seasonality in algal blooms, 

particularly within the freshwater reach. These blooms are more intense in dry years, due 

to increased river residence time, which presents the algal community the opportunity to 

more fully exploit the nutrients supplied by local point and nonpoint, upstream and 

atmospheric sources. Because nutrient load is inextricably linked to stream runoff and 

river flow (nutrient load = concentration x flow), this leads to the irony that as total 

annual nutrient load increases, mean annual algal biomass decreases. During dry years, 

when total nutrient exploitation is achieved, algal biomass, measured as chlorophyll a, 

can exceed 150 mg/m3

 in the riverKs freshwater reach. 

Nitrogen usually appears to be the first limiting macro-nutrient to algal growth in the

freshwater reach. (In actuality, silica is almost invariably the first limiting macronutrient, and the disappearance of bioavailable silica signals the initiation of the blue 

green dominated growth phase (Schelske and Aldridge, 1997).) However, due to the 

presence of nitrogen-fixing blue green algae, growth invariably continues beyond the 

point of nitrogen limitation. This growth, supplemented by N-fixation, can result in an 

appreciable amount of internal nitrogen load, at times doubling the external load-supplied 

concentration. At phosphorus concentrations presently observed in the freshwater LSJR, 

phosphorus limitation of the algal community is only achieved in dry, long residencetime years. When the algal community is phosphorus limited for an extended period, on 

the order of several weeks, a precipitous bloom crash occurs. Extreme low dissolved 

oxygen levels are associated with these bloom crashes. 

To quantify harmful effects of algal blooms, plankton (microscopic plants and animals

that constitute the foundation of the riverKs aquatic food chain) monitoring data were 

analyzed to determine potential disruptions in food web interactions during algal bloom

St. Johns River Water Management District iii
events (Phlips and Cichra, 2002). These data demonstrated that when algal blooms

exceed chlorophyll a concentrations of 40 mg/m3, the phytoplankton community 

becomes dominated by only a few blue-green algal species, and the numbers of beneficial 

zooplankton, representative of the 2nd trophic level, begin to decline. When blooms in 

excess of 40 mg/m3

 chlorophyll a persist for more that 40 days, significant declines in the

numbers of copepod and cladoceran zooplankton are observed. In addition, when 

chlorophyll a of ambient river samples exceeded concentrations of 40 mg/m3 in nutrient 

enrichment incubations, the possibility of high concentrations of the algal toxin 

microcystin increased dramatically (Paerl et al. and Carmichael, 2002). From these 

observations, an algal biomass target for the freshwater LSJR was derived that specified 

chlorophyll a concentrations not exceed 40 mg/m3

 for continuous durations longer than 

40 days. Additional analysis of bloom duration O intensity data estimated a peak

chlorophyll a associated with a 40 day, above 40 mg/m3

 bloom of 70 mg/m3. 

LSJR Predominantly Marine Reach 

When the LSJRQs freshwater phytoplankton are exposed to salinities as low as 2 ppt, 

transformations begin to occur in community composition and physiological processes. 

These transformations have important effects on the aggregate properties of the algae, 

and are manifested in biomass attained and rates of nutrient utilization and 

remineralization. Because of this transformation, an entirely different algal community 

resides in the predominantly marine reach of the river. In the Atlantic Ocean near the 

riverQs mouth, a community dominated by marine forms of the diatom division of algae 

exists. In the mildly salty portion of the river, from the southern Duval County line north 

to the Fuller Warren Bridge, a mixed community of salt-tolerant blue greens, 

dinoflagellates and diatoms are present (Phlips and Cichra, 2002). 

In the narrow, 25-mile, narrow stretch of river connecting these zones, conditions of

water column turbulence and mixing, reduced light, and rapidly changing salinity are 

unfavorable for either of these algal communities. When steep, salinity-induced declines

in the algal community occur just ahead or in the upper portion of this narrowest and 

deepest portion of the river (approximately from river mile 20 to 10, located adjacent to 

St. Johns River Water Management District iv
the downtown Jacksonville stretch of the river), low concentrations of dissolved oxygen 

result that can lead to large fish kills, as was observed in July and August of 1999. The

import of Atlantic, near-coastal blooms during reverse-flows may also negatively affect

oxygen levels in this reach, due to the changes in river channel dimensions that lead to 

reduced photic zone and surface reaeration area. 

Oxygen deficits in the mesohaline reach of the river appear to be largely influenced by 

processes of the algal community, and levels of algal biomass, either imported or

produced within this reach of the LSJR are significantly, positively correlated with the 

general levels of oxygen deficit that occur in a given year. Inorganic nitrogen and 

phosphorus concentrations in this reach almost always exist at levels in excess of what 

could be considered indicative of nutrient limitation, and only approach limiting levels in 

the near coastal waters of the Atlantic, thus large decreases in upstream and local nutrient 

load may be necessary to limit algal growth to acceptable levels. Unlike the blooms

imported to the freshwater LSJR, which can expand due to favorable conditions of light 

and nutrient supply downstream of Palatka, the salinity-transformed algal community in 

the marine reach arises from within this zone or from the near-coastal Atlantic. Local 

loads do not contribute to the expansion of the imported, freshwater algal community, 

which is usually in decline due to salinity stress. Because of this, local nutrient loads can 

be viewed as contributing to a distinctly different algal community. 

The reduction of algal detritus and live algal biomass loading to prevent low oxygeninduced mortality in the fish community was established as the nutrient load reduction 

target for the marineKinfluenced LSJR. Because of concern regarding the appropriateness 

and achievability of the State Standard of 5 mg/L daily average or 4 mg/L instantaneous 

for a blackwater estuary such as the lower St. Johns, the approach for evaluating potential 

estuarine fish mortality described in the recently published EPA guidance, Ambient 

Aquatic Life Water Quality Criteria for Dissolved Oxygen (Saltwater): Cape Cod to Cape

Hattaras was instead used to evaluate detrimental episodes of low dissolved oxygen. 

This approach utilizes established low oxygen duration K intensity tolerances of estuarine 

fish, and allows for some excursions of oxygen below the Florida State Standards if they 

St. Johns River Water Management District v
are not severe enough to result in fish death. Applying the approach detailed in the 

guidance document for evaluating persistent, chronic impairment in estuarine fish 

communities, 3 out of the 6 years of data collected at Dames Point from 1996 through 

2001 exhibited continuous low dissolved oxygen episodes severe enough to result in fish 

community impairment. Based on this result, it is believed that this reach of the river can 

benefit from reductions in loading of algal detritus and nutrients that can lead to the 

growth of marine algal communities. 

Acknowledgements 

Special recognition goes to the following researchers that have pioneered the concepts on 

which the analysis of eutrophication effects described in this report, and the TMDL and 

PLRG targets, have been based. 

Drs. Claire Schelske and Rick Aldridge, who conducted some of the earliest river 

primary production experiments, and the first nutrient enrichment assays to identify the 

patterns of silica and nitrogen limitation in the LSJR. 

Dr. Ed Phlips and Ms. Mary Cichra, who performed years of plankton monitoring and 

analysis to describe the cascade of algal communities associated with salinity and nutrient 

regimes, and did the first quantification of river N-fixation. 

Drs. Hans Paerl and Michael Piehler, who further investigated and quantified the spatial 

and temporal patterns in blue green N-fixation, specific blue green species growth 

adaptations, and confirmed the negative effects on high blue green biomass on 

zooplankton grazing. 

Mr. John Burns and Dr. Wayne Charmichael, who first investigated the presence of blue 

green algal toxins in the freshwater LSJR. 

St. Johns River Water Management District vi
TABLE OF CONTENTS 

EXECUTIVE SUMMARY ............................................................................................. ii 

INTRODUCTION ............................................................................................................1 

ALGAL BIOMASS PATTERNS AND WATER QUALITY EFFECTS RELATED TO 

EUTROPHICATION........................................................................................................6 

Patterns of Nutrient Partitioning and Algal Growth of the Freshwater LSJR ..............6 

Algal Biomass Patterns.............................................................................................6 

Phytoplankton Nutrient Utilization Patterns and Community Composition ..........12 

Frequency of Occurrence and Duration of Algal Biomass.....................................23 

Algal Bloom Characteristics of the LSJR Marine Reach .......................................29 

Nutrient Limitations to Marine Phytoplankton Community Growth .....................40 

Patterns in Oxygen Deficits....................................................................................55 

IMPAIRMENT TARGETS FOR IDENTIFYING TMDL AND PLRG NUTRIENT

REDUCTIONS ...............................................................................................................66 

LSJR Freshwater Targets: Phytoplankton Community Composition Dynamics, 

Zooplankton Interactions and Algal Toxin Production Potential ...............................67 

Freshwater LSJR Algal Biomass Criteria...................................................................68 

Maintenance of Phytoplankton Diversity ...............................................................68 

Facilitation of Upward Trophic Transfer of Primary Production ...........................68 

Algal Toxin Formation Potential ............................................................................70 

Algal Bloom Duration.............................................................................................73 

Marine LSJR Dissolved Oxygen Criteria ...................................................................75 

Dissolved Oxygen Effects.......................................................................................75 

Organism Acute Oxygen Levels.............................................................................76 

Growth Effects........................................................................................................77 

Larval Recruitment .................................................................................................79 

Application of the Criteria ......................................................................................79 

Additional Considerations ......................................................................................81 

Dinoflagellate Bloom Potential...............................................................................82 

RECOMMENDATIONS................................................................................................84 

LITERATURE CITED...................................................................................................87 

St. Johns River Water Management District vii
List of Figures 

Figure 1 The lower St. Johns River Basin .......................................................................2 

Figure 2 The Predominantly Freshwater Reach...............................................................7 

Figure 3 Spatial-temporal pattern in Chlorophyll a, 1995...............................................8 

Figure 4 Spatial-temporal pattern in Chlorophyll a, 1996...............................................8 

Figure 5 Spatial-temporal pattern in Chlorophyll a, 1997...............................................9 

Figure 6 Spatial-temporal pattern in Chlorophyll a, 1998...............................................9 

Figure 7 Spatial-temporal pattern in Chlorophyll a, 1999.............................................10 

Figure 8 Annual TP load and Annual Chlorophyll-a ....................................................11 

Figure 9 Patterns at Racy Point, 1995............................................................................13 

Figure 10 Patterns at Racy Point, 1996..........................................................................14 

Figure 11 Patterns at Racy Point, 1997..........................................................................15 

Figure 12 Patterns at Racy Point, 1998..........................................................................16 

Figure 13 Patterns at Racy Point, 1999..........................................................................17 

Figure 14 Patterns at Racy Point, 2000..........................................................................18 

Figure 15 Patterns at Racy Point, 2001..........................................................................19 

Figure 16 Phytoplankton Bloom Status and Dissolved Oxygen Levels........................22 

Figure 17 Particulate Nutrient Forms and Chlorophyll a Concentrations.....................24 

Figure 18 Boundary Relationships.................................................................................25 

Figure 19 Frequency Distributions ................................................................................26 

Figure 20 Durations of Algal Blooms............................................................................28 

Figure 21 Water Quality and Plankton Monitoring Stations.........................................30 

Figure 22 Change in Phytoplankton Community Richness............................................32 

Figure 23 Mean Number of Phytoplankton Species......................................................32 

Figure 24 Total Chlorophyll a Concentrations..............................................................34 

Figure 25 Total Algal Biovolume ..................................................................................36 

Figure 26 Calculated OrganicCarbon to Biovolume Conversion..................................39 

Figure 27 Silica Concentrations and Diatom Biovolume ..............................................41 

Figure 28 Mean Relative Abundance of Dinoflagellates Biovolume............................43 

Figure 29 Cumulative Frequency Distribution of Inorganic N and P............................48 

St. Johns River Water Management District viii
Figure 30 Time Series Plots of Total Inorganic Nitrogen Concentrations ....................49 

Figure 31 Time Series Plots of Orthophosphate Concentrations...................................51 

Figure 32 Total Dissolved P at Fulton Point..................................................................53 

Figure 33 Historic Change in Dissolved Oxygen Levels...............................................56 

Figure 34 Mean Daily Mid-depth Dissolved Oxygen Concentrations .........................57 

Figure 35 Mean Daily Dissolved Oxygen .....................................................................60 

Figure 36 Longitudinal Dissolved Oxygen Saturation Pattern......................................62 

Figure 37 Daily Mean Oxygen Saturation Deficit.........................................................63 

Figure 38 Direction and Magnitude of Change in Chlorophyll a................................. 63 

Figure 39 Blue Green Relative Abundance ...................................................................69 

Figure 40 Mesozooplankton Response to Algal Biomass .............................................69 

Figure 41 Total Chlorophyll a and Copepod / Cladoceran............................................71 

Figure 42 Annual Trend.................................................................................................71 

Figure 43 Microcystin Concentrations...........................................................................72 

Figure 44 Copedod and Cladocern Zooplankton...........................................................73 

Figure 45 Bloom Maximum Chlorophyll a Concentration............................................74 

Figure 46 Total Chlorophyll a at Racy Point.................................................................76 

Figure 47 Long term chronic exposure threshold relationship ......................................80

St. Johns River Water Management District ix
List of Tables 

Table 1. Top Ten Spring-Summer Freshwater Phytoplankton Based 

 on Biovolume at Racy Point from 1998 D 2001 ..............................................20 

Table 2. Top Ten Marine Phytoplankton Based on Biovolume Observed 

 at Fulton Point, 1998 D 2001.............................................................................31 

Table 3. Comparison of Relative Abundance of Major Phytoplankton 

 Groups from the Fresh and Marine Reaches of the LSJR ................................31 

Table 4. Principle Dinoflagellate Phytoplankton Observed During 

 Episodes of Peak Dinoflagellate Biomass ........................................................44 

Table 5. Fish Species Know to be Present in the LSJR Estuary That 

 are Represented in Studies Upon Which the EPA Estuarine 

 Dissolved Oxygen Guidance is Based ..............................................................78 

St. Johns River Water Management District x
INTRODUCTION 

The St. Johns River is one of the largest blackwater rivers of the southeast U.S. The river

is located in northeast Florida and drains the northeast 1/5th of the state, encompassing a 

9,562 square mile drainage area. The river is slow moving, and is essentially at sea level 

for its final 120 miles. The lower St. Johns is the estuarine portion of the river, formed at 

the confluence of the middle St. Johns and the Ocklawaha River, and encompassing a 

2,750 square mile area (Figure 1). Within this reach, the St. Johns River is slightly more 

that 100 miles long and has a water surface area, including tributary mouths below head 

of tide, of 85,000 acres. 

The lower St. Johns can be divided into three riverine salinity and limnologic zones: a 

fresh tidal lacustrine zone which extends from the city of Palatka north to approximately

the mouth of Black Creek; a predominantly oligohaline, lacustrine zone extending from

Black Creek northward to the Fuller Warren Bridge (I-95) in Jacksonville; and a 

meso/polyhaline, riverine zone downstream to the mouth. The slow moving, lacustrine 

nature of the river facilitates phytoplankton primary production, and spring and summer

algal blooms in this nutrient-rich river often exhibit chlorophyll a concentrations 

exceeding 100 Pg/L. Due to a long history of development within the basin, and its 

associated water quality problems, the LSJR was one of the StateZs originally identified

Surface Water Improvement and Management Act (SWIM; Chapter 373.451, F.S.) water 

bodies for restoration, and has been identified as a high priority water body for the 

establishment of TMDLs and PLRGs to limit nutrient pollution. 

Background 

Accelerated eutrophication due to nutrient enrichment of estuaries represents one of the 

most significant water quality problems faced by near coastal waters world-wide 

(National Research Council, 2000). Investigation into the effects of nutrient enrichment 

and elevated levels of algal biomass in the LSJR has, however, revealed noteworthy 

departures from the eutrophication paradigm established for other estuaries. The LSJR is, 

St. Johns River Water Management District 
Figure 1. The lower St. Johns River Basin. 

St. Johns River Water Management District 2
first, a blackwater river, with large amounts of allochthonous organic carbon and, at 

times, substantial light limitation to primary production imparted by colored dissolved 

organic matter. Also, the broad, shallow zones that exist in the mesohaline reach of most 

river mouth estuaries, and where algal production peaks, are, in the LSJR, due to its 

peculiar morphology, located in the upper, freshwater and oligohaline reaches. This

morphology also results in a very different shape in the zone of oxygen depletion, the 

most often cited manifestation of estuarine eutrophication. Instead of the mesohaline 

zone vertical stratification typical of most eutrophic estuaries, the LSJR Cdead zoneD 

exhibits a stronger longitudinal character, with strong vertical mixing and top to bottom,

long duration, sub-acute low oxygen levels. 

Because of its broad, shallow shape and low flow - long residence time co-occurrence 

with spring and summer enhanced algal growth, the LSJR can exhibit prodigious amount 

of seasonal algal productivity and biomass. River flow, tide, and wind currents 

continually advect, disperse and diffuse algae, nutrients and salinity, with the result that 

the manifestations of nutrient loads frequently occur far from the source of entry. 

Changes in nutrient status, salinity, water column light availability and water temperature 

bring about changing environments that seldom favor one particular algal group, so a 

succession of plankton communities is typically observed through the spring and summer

growth seasons. Environmental stressors can at times be abrupt enough to lead to mass 

death in the algal community, leading to a sequence of water quality characteristics with 

important implications for nutrient recycling, community change, and water quality 

effects. 

Because of these interacting complexities, linking anthropogenic nutrient loading to algal 

growth and its adverse water quality requires a computational framework that accounts 

for temporal and three-dimensional spatial variation. For the LSJR TMDL and PLRG 

assessment, the SJRWMD and FDEP have employed the services of the U.S. Army

Corps Environmental Research Development Center to adapt their time varying threedimensional water quality model, CE-QUAL-ICM (Cerco and Cole, 1995), to the LSJR 

estuary. To adapt and parameterize this model, or any model so complex, it is necessary 

St. Johns River Water Management District 3
to have an understanding of the phenomena to be modeled at two levels. First, it is

necessary to have measurements and analysis results that describe the sub-processes 

leading to eutrophication at discrete levels for specific circumstances, for the purpose of 

model set-up and parameterization. Second, to learn from, and ultimately believe the

outcomes of model scenarios, it is necessary to have at least a qualitative understanding 

of how the interplay of various factors will affect river water quality and biological 

responses on a broad scale. 

For a modeling study of eutrophication effects to be successful, it is also necessary to 

have identified the targets of ecosystem restoration, and how these relate to the variables 

at the modelers disposal. Preferably, the restoration targets are based upon an 

understanding of the endemic biological attributes and amplitude of the system. For this

reason, the targets developed herein rely on improving plankton community diversity and 

enhancing upward transfer of primary production to zooplankton and fish, and reducing 

episodes of low dissolved oxygen that may lead to mortality in fish communities. With 

regard to the restoration targets described in this report, it must be kept in mind the 

ecosystem context in which these targets have been developed. From the point of earliest 

recorded floristic history, when William Bartram paddled the LSJR shoreline in 1776, 

until 1970, this was a system with its biological energy supplied from stream and swamp 

runoff and floating aquatic plants. Though the principle species dominance shifted from

water lettuce (Pistia stratioites) in the late 1800Os with the introduction of water hyacinth 

(Eichornia crassipies), the ecosystem is believed to have remained, at least structurally,

essentially the same until approximately 1940. With the advent of increased nutrient 

loading and aquatic weed spraying from the late 1940Os to Operation Clean Sweep in 

1970 (a concerted aerial spraying effort with 2,4-D to UeradicateV water hyacinth), 

autochthonous primary production has shifted from dominance by macrophytes, to 

dominance by phytoplankton (Moody, 1970). The framework for the LSJR TMDL 

assumes that it will remain a plankton-dominated system. This framework in many ways 

invalidates the restoration approach that relies on the return of the system toward its 

natural, pre-colonial state. 

St. Johns River Water Management District 4
It is the objective of this report to present data and analysis that forms the foundation of 

our understanding on the spatial, seasonal and inter-annual patterns in nutrient 

enrichment effects in the LSJR. In addition, we describe, confirm and quantify plankton 

community phenomena of the LSJR for revision of existing coefficients, or addition of 

algorithms to the CE-QUAL-ICM eutrophication model. These include in particular: 

blue green nitrogen fixation; carbon, nitrogen and phosphorus stoichiometric 

relationships; algal bloom senescence; phytoplankton L zooplankton interactions; and 

algal group differentiation. In the analysis results, various data sets collected from 

between 1994 through 2001 have been used. Although the intervals of data collection 

may be inconsistent with the established TMDL and PLRG modeling time frame of 1995 

through 1999, the findings are beneficial for distinguishing general relationships and 

patterns in algal biomass and nutrients that are expected to be valid at all times. Time

intervals have varied primarily to allow for the incorporation of relevant data that have 

been made available through the evolution of monitoring programs and completion of 

specific studies. 

St. Johns River Water Management District 5
ALGAL BIOMASS PATTERNS AND WATER QUALITY EFFECTS RELATED TO 

EUTROPHICATION 

Patterns of Nutrient Partitioning and Algal Growth of the Freshwater LSJR 

Algal Biomass Patterns 

The slow moving, lacustrine nature of the freshwater LSJR (Figure 2) facilitates 

phytoplankton production, and spring and early summer rainfall deficits, which co-occur 

with increased day length and water temperature, lead to algal blooms within this reach, 

typically attaining peak chlorophyll a concentrations exceeding 100 mg/m3

. Maximum

biomass is reached between May and August. From an annual temporal perspective, the 

pattern in productivity is somewhat analogous to that observed in most Virginian and 

Georgian province estuaries, in which nutrient-rich runoff following late winter snowmelt 

or rain fills the estuary, and then this water mass, slowed and largely retained owing to 

spring drought, is capable of high degree nutrient exploitation and high algal standing 

stock. 

Examination of the annual spatial and temporal pattern in chlorophyll a concentration 

(Figures 3 Z 7) reveals that blooms generally arise simultaneously throughout the river in 

the spring. Only in 1998, a high flow year following a El Nino fall and winter in 1997-

98, did blooms appear to have a strong longitudinal transport character. In general, algal 

biomass is high departing Lake George, and exhibits some decline in standing stock as it 

traverses the narrower, riverine reach to Palatka, then expands again to form a second 

peak between Federal Point and Picolata (Figure 2). Due the long residence time and 

tremendous productivity potential of the upstream Lake George, spring blooms generally 

exit the lake nitrogen and phosphorus limited (Paerl et al, 2002). These blooms are 

capable of further expansion in the LSJR due to favorable photic zone to volume ratios of 

the broad river, and the fresh influx of nutrients from within-basin sources (Phlips and 

Cichra, 2000). From 1995 Z 1999, the mean concentration of total phosphorus entering 

the LSJR at Buffalo Bluff was 0.063 mg/L, while mean concentration for the same time

St. Johns River Water Management District 6
Figure 2. The Predominantly Freshwater Reach of the Lower St. Johns River. 

Shands Br.

Palatka 

Lake 

George

Watson Isl.

Racy Point 

Federal Point

Mouth of Black 

Creek 

(downstream 

boundary) 

Buffalo Bluff 

(upstream 

boundary) 

St. Johns River Water Management District 7
Figure 3. Spatial-Temporal Pattern in Chlorophyll a in the Lower St. Johns River, 1995. 

Data collected in a bi-weekly water quality monitoring program, typically during the 2nd

and 4th weeks of each month. X axis refers to month and week of sampling, and Z axis to 

location, with most upstream station against the back wall. Some values interpolated 

when sampling done monthly. 

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

Fulton Pt.

Talleyrand

Piney Pt.

Mandarin

Hibernia

Picolata

Watson Isl.

Racy Pt.

Federal Pt.

Palatka L. George

0

20

40

60

80

100

120

140

160 Chlorophyll-a, mg/m3

Bi-weekly Interval

1995

Fulton Pt.

Talleyrand

Piney Pt.

Mandarin

Hibernia

Picolata

Watson Isl.

Racy Pt.

Federal Pt.

Palatka

L. George

Figure 4. Spatial-Temporal Pattern in Chlorophyll a in the Lower St. Johns River, 1996. 

Data collected in a bi-weekly water quality monitoring program, typically during the 2nd

and 4th weeks of each month. X axis refers to month and week of sampling, and Z axis to

location, with most upstream station against the back wall. Some values interpolated 

when sampling done monthly. 

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

Fulton Pt.

Talleyrand

Piney Pt.

Mandarin

Hibernia

Shands Br.

Watson Isl.

Racy Pt.

Federal Pt.

Palatka

L. George

-40

10

60

110

160

Chlorophyll-a, mg/m3

Bi-weekly Interval

1996

Fulton Pt.

Talleyrand

Piney Pt.

Mandarin

Hibernia

Shands Br.

Watson Isl.

Racy Pt.

Federal Pt.

Palatka

L. George

St. Johns River Water Management District 8
Figure 5. Spatial-Temporal Pattern in Chlorophyll a in the Lower St. Johns River, 1997. 

Data collected in a bi-weekly water quality monitoring program, typically during the 2nd

and 4th weeks of each month. X axis refers to month and week of sampling, and Z axis to

location, with most upstream station against the back wall. Some values interpolated 

when sampling done monthly. 

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

Fulton Pt.

Talleyrand

Piney Pt.

Mandarin

Hibernia

Shands Br.

Watson Isl.

Racy Pt.

Federal

Palatka

L. George

0

20

40

60

80

100

120

140

160 Chlorophyll-a, mg/m3

Bi-weekly Interval

1997

Fulton Pt.

Talleyrand

Piney Pt.

Mandarin

Hibernia

Shands Br.

Watson Isl.

Racy Pt.

Federal

Palatka

L. George

Figure 6. Spatial-Temporal Pattern in Chlorophyll a in the Lower St. Johns River, 1998. 

Data collected in a bi-weekly water quality monitoring program, typically during the 2nd

and 4th weeks of each month. X axis refers to month and week of sampling, and Z axis to 

location, with most upstream station against the back wall. Some values interpolated 

when sampling done monthly. 

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

Fulton

Talleyrand

Piney Pt.

Mandarin

Hibernia

Shands

Watson Isl.

Racy Pt.

Federal Pt.

Palatka

L.George

0

20

40

60

80

100

120

140

160 Chlorophyll-a, mg/m3

Bi-weekly Interval

1998

Fulton

Talleyrand

Piney Pt.

Mandarin

Hibernia

Shands

Watson Isl.

Racy Pt.

Federal Pt.

Palatka

L.George

St. Johns River Water Management District 9
Figure 7. Spatial-Temporal Pattern in Chlorophyll a in the Lower St. Johns River, 1999. 

Data collected in a bi-weekly water quality monitoring program, typically during the 2nd

and 4th weeks of each month. X axis refers to month and week of sampling, and Z axis to

location, with most upstream station against the back wall. Some values interpolated 

when sampling done monthly. 

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

Fulton Pt.

Talleyrand

Piney Pt.

Mandarin

Hibernia

Shands Br.

Watson Isl

Racy Pt.

Federal Pt.

Palatka

L. George

0

20

40

60

80

100

120

140

160 Chlorophyll-a, mg/m3

Bi-weekly Interval

1999

Fulton Pt.

Talleyrand

Piney Pt.

Mandarin

Hibernia

Shands Br.

Watson Isl

Racy Pt.

Federal Pt.

Palatka

L. George

period at Racy Point, approximately 25 miles downstream, was 0.087 mg/L, and increase 

of 38%. 

In most years, chlorophyll a falls dramatically downstream of Shands Bridge, coinciding 

with the gradual salinity-induced transformation of the plankton community. This decline 

is brought about by a combination of salinity stress, increased zooplankton grazing, and 

finally, reduced hydraulic residence time. Salinities can vary considerably, and upstream 

inputs of brackish artesian spring water can also push total dissolved solids concentration 

to nearly 1 ppt during drought without marine influence. During the severe drought years 

of 2000 and 2001, marine salinity was seen to encroach upstream as far as RKm 100, or 

near Racy Point. 

In the 5-year modeling time window for LSJR TMDL/PLRG development, springsummer algal biomass was the lowest in the 1995 high-flow year and greatest in the 1999 

low-flow year. Prevailing river flow and its control over residence time within the 

freshwater reach is the most important factor controlling the inter-annual variation in 

St. Johns River Water Management District 10
algal bloom intensity and duration. Mean residence time is around one month, although 

flow regimes between 1995 and 2001 have seen water replacement occur in less than 10 

days (March 1998), to conditions where water was essentially static (August 1999). 

River flow controls phytoplankton biomass, as it co-varies with a suite of factors that can 

account for the potential of the algal community to optimize bioavailable nutrient supply. 

High flows typically occur in fall and winter, when cooler water temperatures and shorter 

irradiance duration reduces production, and higher terrestrial runoff imports greater 

amounts of colored aquatic humic substances, thus increasing light attenuation. Higher 

flow also shortens segment residence time, reducing the time for nutrient depletion and 

phytoplankton community maturation. Because nutrient load is linked to river residence 

time through discharge, the irony exists that as nutrient load increases, mean annual

chlorophyll a decreases (Figure 8). 

Figure 8. Relationship between Annual TP Load to the Freshwater LSJR and Mean 

Annual Chlorophyll-a Concentration, 1995-99. Square represents projected mean annual 

chlorophyll-a at a hypothetical zero terrestrial flow setting, and this point is included in

the regression equation. 

 

Racy Point, 1995-99

y = -0.0648x + 73.526

R2

 = 0.8775

0

10

20

30

40

50

60

70

80

0 100 200 300 400 500 600 700 800 900

Mean Annual TP Load, MT/yr

Mean Annual Chl a, mg/m3

St. Johns River Water Management District 11
Phytoplankton Nutrient Utilization Patterns and Community Composition 

The effect of the interplay of factors regulating the creation and sequestration of carbon 

and nutrients by phytoplankton can be seen in Figures 9 ? 15. These annual time series 

plots of chlorophyll a, total nitrogen, phosphorus cell quota (estimated with particulate P 

to algal C ratio) and inorganic nutrient concentrations for the Racy Point station (located 

at the midpoint of the freshwater reach) demonstrate the control of river nutrient 

concentrations by phytoplankton growth patterns. With the exception of 1997, 

chlorophyll a can be seen to exhibit at least one pronounced peak during the year. The 

absence of such a peak in 1997 is due to the effects of a spill of mine tail-water that 

contributed a large , extremely turbid and humic-stained plume to the river in the vicinity 

of Racy Point on about April 30th of that year. This event dramatically reduced the photic

zone, and effectively curtailed the spring bloom. The timing and number of bloom peaks 

is largely dependent upon river flow. Under a low to moderate flow condition, the first 

bloom peak will occur in May; under extreme low flows, (as occurred in 1999 ? 2001), 

multiple bloom peaks can be observed. Under higher flow conditions, the bloom peak 

may be delayed until July. 

Algal taxonomic information, available for years 1998 ? 2001 (Table 1) reveals the 

community succession pattern responsible for patterns in algal biomass and nutrient 

partitioning. Diatom species dominate the phytoplankton assembledge until the spring or 

summer bloom season. Common diatom genera seen at this time are Melosira, 

Merismopedia, and Fragilaria. When chlorophyll a surpasses concentrations of 

approximately 40 mg/m3

, blue green species begin to dominate. The end of diatom

dominance occurs coincident with dissolved silica falling to very low levels, suggesting 

silica limitation as an important trigger for the onset of blue green dominance (Schelske 

and Aldridge, 1997). Typically, the non-N-fixing blue green Microcystis will be present 

in the community as diatom dominance ends, but it is supplanted soon by the N-fixing 

Anabaena when assimilable inorganic nitrogen is depleted. This usually corresponds to 

total inorganic N (NH4 +NOX) concentration being less than 0.020 mg/L. Pronounced 

spikes in river total N coincident with algal biomass peaks support the phenomena of 

St. Johns River Water Management District 12
Figure 9. Patterns in Chlorophyll a, total nitrogen, calculated phosphorus cell quota and inorganic nutrients at Racy Point, 1995. 

0.000.010.020.030.040.050.060.070.080.090.10

11/30 1/29 3/30 5/29 7/28 9/26 11/25

Particulate P/Algal C

Est. Cell P:C

0

0.020.040.060.08

0.1

0.120.140.16

11/30 1/29 3/30 5/29 7/28 9/26 11/25

Concentration, mg/L

PO4TINSiO2/100

1995

0

80604020

160140120100

11/30 1/29 3/30 5/29 7/28 9/26 11/25

, mg/m Chlorophyll a

3

Chlorophyll-a

0

0.

1

5

1.

2

5

2.

3

5

3.5

11/30 1/29 3/30 5/29 7/28 9/26 11/25

 mg/L, Total N

Total N

St. Johns River Water Management District 13
Figure 10. Patterns in Chlorophyll a, total nitrogen, calculated phosphorus cell quota and inorganic nutrients at Racy Point, 1996. 

1996

0

80604020

160140120100

11/27 1/26 3/26 5/25 7/24 9/22 11/21

Chlorophyll a, mg/m

3

Chlorophyll-a

0.000.010.020.030.040.050.060.070.080.090.10

11/27 1/26 3/26 5/25 7/24 9/22 11/21

Particulate P/Algal C

Est. Algal P/C

0

0.020.040.060.08

0.1

0.120.140.16

11/27 1/26 3/26 5/25 7/24 9/22 11/21

Concentration, mg/L

TINPO4Diss. SiO2/100

0

0.

1

5

1.

2

5

2.

3

5

3.5

11/27 1/26 3/26 5/25 7/24 9/22 11/21

L mg/ on, Concentrati

Total N

St. Johns River Water Management District 14
Figure 11. Patterns in Chlorophyll a, total nitrogen, calculated phosphorus cell quota and inorganic nutrients at Racy Point, 1997. 

1997

0

80604020

160140120100

12/1 1/30 3/31 5/30 7/29 9/27 11/26

/mg m, ll a ophy lorhC

3

Chlorophyll a

0

0.020.040.060.08

0.1

0.120.140.16

12/1 1/30 3/31 5/30 7/29 9/27 11/26

Concentration, mg/L

TINPO4Diss. SiO2/100

0.000.010.020.030.040.050.060.070.080.090.10

12/1 1/30 3/31 5/30 7/29 9/27 11/26

Particulate P/Algal C

Est. Algal P/C

0

0.

1

5

1.

2

5

2.

3

5

3.5

11/27 1/26 3/26 5/25 7/24 9/22 11/21

Concentration, mg/L

Total N

St. Johns River Water Management District 15
Figure 12. Patterns in Chlorophyll a, total nitrogen, calculated phosphorus cell quota and inorganic nutrients at Racy Point, 1998. 

0.000.010.020.030.040.050.060.070.080.090.10

11/16 1/5 2/24 4/15 6/4 7/24 9/12 11/1 12/21

Particulate P/Algal C

Estimated Cell P:C

0

80604020

160140120100

11/16 1/5 2/24 4/15 6/4 7/24 9/12 11/1 12/21

m mg/ on, Concentrati

3

Chlorophyll-a 1998

0

0.

1

5

1.

2

5

2.

3

5

3.5

11/16 1/5 2/24 4/15 6/4 7/24 9/12 11/1 12/21

L mg/ on, Concentrati

Total N

0

0.020.040.060.08

0.1

0.120.140.16

11/16 1/5 2/24 4/15 6/4 7/24 9/12 11/1 12/21

Nutrient, mg/L

TINPO4Diss. SiO2/10

St. Johns River Water Management District 16
Figure 13. Patterns in Chlorophyll a, total nitrogen, calculated phosphorus cell quota and inorganic nutrients at Racy Point, 1999. 

0

80604020

160140120100

12/1 1/30 3/31 5/30 7/29 9/27 11/26

m/ mg,no trati cenn Co

3

Chlorophyll-a 1999

0.000.010.020.030.040.050.060.070.080.090.10

12/1 1/30 3/31 5/30 7/29 9/27 11/26

gal Cl Particulate P/A

Estimated Cell P:C

0

0.5

1

1.5

2

2.5

3

3.5

12/1 1/20 3/11 4/30 6/19 8/8 9/27 11/16

L mg/ on, Concentrati

Total N

0

0.020.040.060.08

0.1

0.120.140.16

11/11 12/31 2/19 4/10 5/30 7/19 9/7 10/27 12/16

Concentration, mg/L

TINPO4Diss. SiO2/10

St. Johns River Water Management District 17
Figure 14. Patterns in Chlorophyll a, total nitrogen, calculated phosphorus cell quota and inorganic nutrients at Racy Point, 2000. 

0

0.020.040.060.08

0.1

0.120.140.16

12/1 1/30 3/30 5/29 7/28 9/26 11/25

Concentration. mg/L

TINPO4Diss. SiO2/10

0.000.010.020.030.040.050.060.070.080.090.10

12/1 1/30 3/30 5/29 7/28 9/26 11/25

Particulate P:Algal C

Estimated Cell P:C 2000 

0

80604020

160140120100

12/1 1/30 3/30 5/29 7/28 9/26 11/25

m mg/ on, Concentrati

3

Chlorophyll-a

0

0.

1

5

1.

2

5

2.

3

5

3.5

12/1 1/30 3/30 5/29 7/28 9/26 11/25

L mg/ on, Concentrati

Total N

St. Johns River Water Management District 18
Figure 15. Patterns in Chlorophyll a, total nitrogen, calculated phosphorus cell quota and inorganic nutrients at Racy Point, 2001. 

0

0.020.040.060.08

0.1

0.120.140.16

11/30 1/29 3/30 5/29 7/28 9/26 11/25

oncentration. mg/LC

PO4TINDiss. SiO2/10

0.000.010.020.030.040.050.060.070.080.090.10

11/30 1/29 3/30 5/29 7/28 9/26 11/25

Particulate P:Algal C

Estimated Cell P:C 2001

0

80604020

100120140160

11/ 30 1/ 29 3/ 30 5/ 29 7/ 28 9/ 26 11/ 25

Chlorophyll a

0

0.

1

5

1.

2

5

2.

3

5

3.5

11/30 1/29 3/30 5/29 7/28 9/26 11/25

Concentration, mg/L

TN

St. Johns River Water Management District 19
Table 1. Top 5 most abundant phytoplankton by biovolume during Spring-Summer sampling at Racy Point, 1998-2001. Values to the

left of scientific names are biovolume, Pm3* (mL x 1000)-1. Numbers in bold below each sampling event column represent the percent of total biovolume represented by the top 5 phytoplankton. Bottom rows are mean and standard error of the percent monthly 

top 5 dominance. 

March April May June July August September October 

4/2/1998 4/27/1998 5/26/1998 6/30/1998 8/3/1998 8/24/1998 9/22/1998 10/28/1998 

220 Melosira 124 Fragilaria 2086 Unid. Chrysophyta 745 Lyngbya 1817 Oscillatoria 3219 Oscillatoria <2μm 2326 Oscillatoria <2μm 1174 Oscillatoria137 Unid. Cryptophyta 98 Unid. Cryptophyta 442 Melosira 616 Anabaena 1255 Anabaena 647 Cylindrospermopsis 756 Microcystis 273 Unid. Centric Diat. 

53 Fragilaria 79 Unid. Centric Diat. 290 Microcystis aerug. 368 Unid. Chrysophyta 680 Ocillatoria 453 Melosira 464 Unid. Centric Diat. 215 Microcystis 41 Unid. Centric Diat. 71 Melosira 172 Anabaena 324 Microcystis 436 Unid. Pennate Dait. 432 Microcystis 340 Ocillatoria 211 Microcystis 33 Unid Chlorophyta 66 Unid. Chlorophyta 161 Lyngbya 293 Anabaena 390 Lyngbya 340 Ocillatoria 316 Microcystis 155 Thalassiosira 

737 65.7 1058 41.5 3954 79.7 4090 57.4 8694 52.7 8385 60.7 7111 59.1 3848 52.7 

3/30/1999 4/29/1999 5/27/1999 6/29/1999 7/27/1999 8/26/1999 9/23/1999 10/26/1999

3057 Oscillatoria <2μm 3713 Oscillatoria <2μm 7389 Oscillatoria <2μm 572 Oscillatoria <2μm 923 Cylindrospermopsis 8651 Oscillatoria <2μm 6164 Oscillatoria <2μm 2811 Oscillatoria <2μm 

376 Anabaena 3559 Anabaena 6747 Cylindrospermopsis 172 Microcystis 504 Lyngbya contorta 5388 Cylindrospermopsis 480 Ocillatoria 1071 Melosira (Aulac.)200 Microcystis 700 Melosira (Aulac.) 1474 Anabaena 153 Meris. tenuissima 502 Microcystis 1391 Unid. Centric Diat. 291 Cylindrospermopsis 560 Microcystis 158 Aphanizomenon 432 Anabaena 431 Unid. Centric Diat. 138 Unid. Cryptophyta 476 Ocillatoria 712 Unid. Centric Diat. 281 Lyngbya contorta 444 Lyngbya contorta117 Unid Centric Diat. 391 Anabaena circinalis 414 Anabaena circinalis 89 Unid. Chlorophyta 275 Lyngbya 641 Pennates 154 Unid. Pennate Dait. 314 Ocillatoria 

5142 76.0 12250 71.8 20294 81.1 1773 63.4 4677 57.3 20981 80.0 8831 83.5 7177 72.5 

3/28/2000 4/25/2000 5/23/2000 6/27/2000 7/25/2000 8/23/2000 9/27/2000 10/30/2000

996 Unid. Chrysophyta 1711 Unid. Chrysophyta 9588 Oscillatoria <2μm 324 Pennates 1904 Oscillatoria <2μm 3436 Oscillatoria <2μm 1144 Oscillatoria <2μm 1279 Oscillatoria <2μm 158 Unid. Centric Diat. 1485 Oscillatoria <2μm 3750 Anabaena 304 Melosira (Aulac.) 494 Melosira (Aulac.) 1046 Cryptophyta 203 Unid. Centric Diat. 506 Unid. Chrysophyta 156 Melosira (Aulac.) 151 Anabaena 1926 Cylindrospermopsis 214 Oscillatoria <2μm 343 Unid. Pennate Dait. 730 Unid. Chrysophyta 165 Unid. Cryptophyta 480 Unid. Centric Diat. 129 Unid. Centric Diat. 95 Unid. Centric Diat. 986 Unid. Pyrrhophyta 190 Unid. Pyrrhophyta 302 Melosira (Aulac.) 529 Aphanizomenon 136 Unid. Pyrrhophyta 379 Unid. Centric Diat. 115 Microcystis 95 Unid. Centric Diat. 596 Anabaena circinalis 190 Unid. Centric Diat. 289 Unid. Pennate Dait. 511 Anabaena 127 Unid. Centric Diat. 332 Unid. Centric Diat. 

3080 51.6 4402 80.3 20145 83.6 2631 46.4 5262 63.3 10171 61.5 2734 64.9 4106 72.5 

3/29/2001 5/1/2001 5/30/2001 6/28/2001 7/23/2001 8/20/2001 9/25/2001 10/24/2001 

2494 Unid. Chrysophyta 1175 Oscillatoria <2μm 6380 Oscillatoria <2μm 8218 Oscillatoria <2μm 2813 Oscillatoria <2μm 6704 Oscillatoria <2μm 1601 Oscillatoria <2μm 113 Lyngbya contorta

174 Anabaena 823 Unid. Chrysophyta 1959 Cylindrospermopsis 2986 Cylindrospermopsis 548 Lyngbya contorta 939 Cylindrospermopsis 272 Fragil. construens 73 Unid. Cryptophyta163 Oscillatoria <2μm 260 Anabaena 486 Ocillatoria 464 Unid. Centric Diat. 475 Unid. Centric Diat. 412 Melosira (Aulac.) 136 Lyngbya contorta 66 Melosira (Aulac.) 117 Ankistrodesmus 153 Unid. Centric Diat. 476 Plagiotropis 333 Ocillatoria 462 Microcystis 352 Ocillatoria 127 Unid. Pyrrhophyta 59 Oscillatoria <2μm

92 Scened. quadricauda 144 Anabaenopsis 402 Plagiotropis 285 Unid. Pennate Dait. 371 Melosira (Aulac.) 326 Lyngbya contorta 101 Rhizosolenia (Freshwater forms) 50 Frag. Construens 

4393 69.2 3917 65.2 12404 78.2 15193 80.9 6492 71.9 10071 86.7 2867 78.0 593 60.9 

65.6 64.7 80.6 62.0 61.3 72.2 71.4 64.6 10.3 16.7 2.3 14.4 8.3 13.1 11.3 9.7 

St. Johns River Water Management District 20
algal N fixation. Phlips and Cichra (2001) identified nitrogen fixation rates in the 

freshwater LSJR during a year 2000 survey, and determined that this pathway is a 

significant contributor to the total segment nitrogen load, and the importance of Nfixation has been subsequently confirmed in growth assays (Paerl et al, 2001). In 1998, a 

single large bloom is seen to occur, with a coincident N concentration spike. In 1999, 

2000 and 2001, double blooms occur, but only in the 1999 bloom is there a nitrogen 

concentration spike associated with the second bloom. 

If low river flow allows for sufficient time for phosphorus limitation to occur, then a 

dramatic collapse of the phytoplankton community can be observed. Such bloom crashes

were observed in 1999 L 2001. These crashes occur 1) in the absence of freshwater 

inflows that could possibly dilute the bloom; 2) before the summer solstice, and hence are 

not attributable to day length reduction senescence; and 3) despite falling numbers of 

bloom-consuming zooplankton. Substantial community shifts can be seen with these 

bloom crashes, with dominance by the N-fixing blue greens Anabaena or 

Cylindrospermopsis giving way to diatoms or Microcystis. Extreme phosphorus 

limitation in the community, estimated in Figures 13(c) L 15(c) by the co-occurrence of

low particulate P:algal C ratio (indicative of low internal phosphorus stores) and low PO4, 

seems to be an important condition for the triggering of these bloom crashes. Minimum

P:algal C ratios during these times were generally in the range of 0.010 - 0.015, and 

values in this range were considered to represent the minimum cell quota for the 

predominantly blue green algal community present at this time. 

Coincident with these precipitous declines in algal standing stock are declines in 

dissolved oxygen (Figure 16a-c) that suggest algal respiration or organic matter 

decomposition, events that would be consistent with rapid bloom senescence. These low

dissolved oxygen levels, often below 3 mg/L for large areas of river, are in a range that is

detrimental to the health of fisheries in this reach. Possible factors for this community

decline include settling, bacterial predation (perhaps facilitated by a nutritionally stressed

phytoplankton community), or physiological stress of extreme nutrient limitation. 

St. Johns River Water Management District 21
Figure 16. Relationship Between Phytoplankton Bloom Status and Low Dissolved 

Oxygen Levels in the Freshwater LSJR. 

 a. 1999

0

20

40

60

80

100

120

140

160

3/1 3/31 5/1 5/31 7/1 7/31 8/31 9/30 10/31

Chlorophyll a, mg/m3, or D.O., 

mg/L x 10

Continuous DO x 10

Racy Pt. Chl. a

Ambient Monitoring D.O.

 b. 2000

0

20

40

60

80

100

120

140

160

2/29 3/30 4/30 5/30 6/30 7/30 8/30 9/29 10/30

Chlorophyll a, mg/m3, or 

D.O., mg/L x 10

Racy Pt. Chlorophyll a

Continuous D.O. x 10

Ambient Monitoring D.O.

 c. 2001

0

20

40

60

80

100

120

140

160

2/28 3/30 4/30 5/30 6/30 7/30 8/30 9/29 10/30

Chlorophyll a, mg/m3, or 

D.O., mg/L x 10

Chlorophyll a 

Amb. Monit. DO x 10

Continuous D.O. x 10

St. Johns River Water Management District 22
Superior nutrient uptake capabilities of some species under extremely low mineral 

nutrient concentrations may also play a role in bloom crashes and re-emergence. 

Because of the strong phytoplankton control over the river=s nutrient partitioning during 

the peak algal growth seasons, particulate organic nutrients are correlated with algal 

biomass on sampling dates when low inorganic nutrient concentrations are observed 

(Figure 17). Particulate organic nutrient concentrations for these dates also agree well 

with the Redfield stoichiometric conversions to algal biomass. The greater amount of 

spread and slight curvilinear nature of the chlorophyll a to particulate phosphorus 

relationship suggests a fair amount of elasticity in growth requirements for phosphorus, 

and this would be expected if phosphorus uptake occurred ahead of present growth needs 

(luxury uptake). 

Comparison of particulate organic carbon to corrected chlorophyll a suggests that a 

conversion factor of 50:1 carbon:chlorophyll a is generally appropriate for LSJR 

freshwater phytoplankton communities (Figure 18(a)). In calculations utilizing 

biovolume measurements, performed when distinguishing the algal carbon within algal 

taxonomic groupings, a conversion of 0.3*biovolume, in μm3

/ml, was used to convert to

algal carbon, in mg/L (Figure 18(b)). 

Frequency of Occurrence and Duration of Algal Biomass 

Chlorophyll a frequency distributions for the three stations residing within the LSJR fresh

reach (Federal Point, Racy Point and Watson Island, at 110, 100 and 90 RKm) are shown 

in Figure 19 for all data and spring and summer data from 1995 through 2001. Because 

algal bloom biomass, measured as chlorophyll a, is skewed toward higher concentrations, 

the values are presented as the natural log of chlorophyll concentration to render the data 

normally distributed. Chlorophyll a tends to exceed 20 mg/m3

 (benchmark associated

with fair trophic condition) 50 Y 75% of the time for all data and 68 - 88% of the time for 

spring Y summer data. Chlorophyll a exceeds 40 mg/m3

 (benchmark associated with

St. Johns River Water Management District 23
Figure 17. Relationship Between Particulate Nutrient Forms for Low Inorganic Nutrient 

Sampling Dates and Chlorophyll a Concentration, 1995-99. Low inorganic nutrient 

concentrations considered to be LE 0.005 mg/L for PO4 and 0.02 mg/L for TIN. Solid 

lines indicate phytoplankton N and P for phytoplankton C:N and C:P of 5.67:1 and 41:1, 

and a C:Chlorophyll a ratio of 50:1. Dashed line is model of Huber et al. (1982). 

Phosphorus

0

20

40

60

80

100

120

140

160

180

0 0.02 0.04 0.06 0.08 0.1 0.12 0.14

Particulate Phosphorus, mg/L

Corr. Chlorophyll a, mg/m3

Racy Pt.

Palatka

Picolata

Nitrogen

0

20

40

60

80

100

120

140

160

180

0 0.5 1 1.5 2 2.5

Particulate Organic N, mg/L

Corr. Chlorophyll a, mg/m3

Racy Pt.

Palatka

Picolata

St. Johns River Water Management District 24
Figure 18. Boundary Relationships Between Particulate Organic Carbon and (a) Total 

Chlorophyll a and (b) Algal Biovolume for LSJR Freshwater Sampling Stations. Vertical 

red line in (a) identifies 50:1 C:chlorophyll-a. Vertical red line in (b) corresponds to 0.3 

microg. C:1000 micro-m3 biovolume. Data from Phlips and Cichra, 2001. 

( a ) POC:Chlorophyll-a 

0

20

40

60

80

100

120

140

160

0 100 200 300 400 500

POC:Chlorophyll a ratio

Total Chlorophyll a, mg/m3

(b) POC:Algal Biovolume

0

5000

10000

15000

20000

25000

30000

0 0.002 0.004 0.006 0.008 0.01 0.012

C:Biovolume Ratio

Biovolume, micro-m3/ml x 

1000

St. Johns River Water Management District 25
Figure 19. Frequency distributions of total and spring-summer total (uncorrected) 

chlorophyll a for LSJR freshwater stations. Ln(20) = 3; Ln(40) = 3.7; Ln(60) = 4.09. 

SprAll 

P

er

ce

nt 

R

an

Ln Tot. Chl a

0.6 0.8 1 1.2 1.4 1.6 1.8 2 2.2 2.4 2.6 2.8 3 3.2 3.4 3.6 3.8 4 4.2 4.4 4.6 4.8 5 5.2 5.4

10

9

8

7

6

5

4

3

2

1

0

Watson Isl. - RKm 90 

All Data

Spr-Sum

P

er

ce

nt 

R

an

Ln Tot. Chl a

0.6 0.8 1 1.2 1.4 1.6 1.8 2 2.2 2.4 2.6 2.8 3 3.2 3.4 3.6 3.8 4 4.2 4.4 4.6 4.8 5 5.2 5.4

10

9

8

7

6

5

4

3

2

1

0

Racy Pt - RKm 100

SprAll 

P

er

ce

nt 

R

an

Ln Tot. Chl a

0.6 0.8 1 1.2 1.4 1.6 1.8 2 2.2 2.4 2.6 2.8 3 3.2 3.4 3.6 3.8 4 4.2 4.4 4.6 4.8 5 5.2 5.4

10

9

8

7

6

5

4

3

2

1

0

Federal Pt. - RKm 110

St. Johns River Water Management District 26
poor trophic status) 18 / 29% of the time for all data and 33 / 49% of the time for spring 

/ summer data. 

The length of time chlorophyll a exceeded 40 mg/m3

 for these stations was sorted in rank

order and again displayed as percent frequency distributions (Figure 20). To determine

the duration of above 40 mg/m3

 concentrations, the proportion of time between sampling 

dates in which concentrations went from below to above or above to below was linearly 

interpolated, and added to the duration for which concentration remained above 40. The

50th percentile duration ranged from 24 to 29 days, while the 75th percentile duration 

ranged from 32 days at Federal point to 76 days at Watson Island. For the 8 years of data 

for which durations were calculated (1994 through 2001), blooms exceeding 40 mg/m3

occurred 21 times at Racy Point, 18 times at Federal Point, and 16 times at Watson 

Island. 

In summary, nutrient control of phytoplankton biomass production within the freshwater 

LSJR is seen to be intermittent and seasonal, coincident with the annual trend in 

phytoplankton productivity, and moderated by river flow. Waters entering the freshwater 

LSJR appear to be predominantly phosphorus limited, but large additions of phosphorus 

in the external load within this reach appear to offset this condition. Only in dry years 

does a condition of phosphorus limitation prevail. When conditions of phosphorus 

limitation occur for extended intervals, the phytoplankton community appears to collapse, 

and this event is associated with severely low levels of dissolved oxygen. While nitrogen 

appears to be the primary limiting nutrient (when nutrients are limiting), N-fixation by 

blue green algae would appear to render P the principle driver of ultimate phytoplankton 

biomass. As such, particulate organic nitrogen is the better indicator of the amount of 

algal biomass, but total phosphorus provides the better indicator of algal community 

expansion potential. 

St. Johns River Water Management District 27
Figure 20. Distribution of durations of algal blooms greater than 40 mg/m3

 total 

chlorophyll a for LSJR freshwater stations. 

Bloom Duration Distribution

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80 90 100 110 120

Bloom duration, days

Percent Rank

RKm 100

RKm 110

RKm 90

St. Johns River Water Management District 28
Algal Bloom Characteristics of the LSJR Marine Reach 

The degree to which marine salinity encroaches into the lower St. Johns River is 

dependent primarily upon river flow, and to a lesser extent on episodic, short term

changes in ocean elevation (Sucsy and Morris, 2001). Under average river flow 

conditions, the greatest upstream advance of marine waters typically occurs in May or

June (the peak of the spring dry season), to the area near the mouth of Black Creek 

(Figure 21). For this reason, this point has been used to distinguish the marine-influenced 

(also referred to in this report as the oligo/mesohaline reach) lower St. Johns from its 

predominantly freshwater section. Few, if any algal species of the freshwater LSJR are 

capable of surviving the transition to the higher salinity environment of the oligohaline 

and mesohaline reaches. This results in a complete changeover in phytoplankton 

community species in marine reaches of the river (Table 2). Unlike the cyanobacterial 

domination of algal biovolume of the freshwater reach, the oligo/mesohaline reach is

dominated by diatoms, with smaller relative amounts of blue greens, and with somewhat 

greater numbers of dinoflagellates (Table 3). 

The zone of salinity-driven phytoplankton community transition appears to extend from 3 

to 18 ppt (Figure 22). The zone of maximum community transition, based upon the 

fewest numbers of phytoplankton in common between same-day longitudinal sampling, 

was found to occur between 18 to 25 ppt. (Figure 23). Because some of the species of the

freshwater blooms imported to the oligohaline and mesohaline river are under salinity 

stress and in decline, the paradox arises such that total algal biomass appears to be lowest

where external nutrient loads are the greatest. It is assumed that nutrient loads within this

reach have little effect on perpetuating the algal biomass expansion of species that are in 

decline through salinity stress, and are instead primarily responsible for nourishing and 

accelerating growth within the river or in near offshore waters for primarily salt-tolerant 

or marine phytoplankton. For this reason, efforts in developing causal relationships 

between nutrient loads and algal growth within the oligohaline and mesohaline reaches

have focused primarily on the effects of these loads to marine blooms. In the process of 

quantifying accelerated algal growth effects and judging load reduction performance, the 

St. Johns River Water Management District 29
Figure 21. Water Quality and Plankton Monitoring Stations of the Oligo/Mesohaline 

Reach of the LSJR. 

Mouth of 

Black Creek 

(Upstream 

boundary) 

Doctors Lake

Dames

Point

Acosta

Bridge

Fulton 

Talleyrand Point

Piney Point

Plummers Cove 

Mandarin Point

St. Johns River Water Management District 30
Table 2. Top 10 Most Predominant Phytoplankton Species based on Biovolume in 

Sampling from the LSJR Stations at Fulton Point (Marine) and Racy Point (Fresh). Data 

from Phlips and Cichra, (2001). 

Rank Racy Point (Freshwater) Fulton Point (Marine) 

1 Oscillatoria <2μm diameter Bellerochea

2 Cylindrospermopsis spp. Rhizosolenia 

3 Anabaena spp. Centric Diatoms < 25m 

4 Microcystis incerta Centric Diatoms >> 100m 

5 Melosira (Aulacoseira) Guinardia flaccida 

6 Ocillatoria (other diameters) Coscinodiscus 

7 Lyngbya contorta Skeletonema 

8 Centric Diatoms < 25m Leptocylindrus 

9 Raphidiopsis Division Cryptophyta 

10 Pennate Diatoms > 25m < 

50m

Gymnodinium spp. 

Table 3. Mean Percent Composition of Algal Functional Groups for LSJR OligoMesohaline Stations During Predominantly Fresh (Total Chloride < 1,500 mg/L) and 

Predominantly Marine (T. Chloride > 1,500 mg/L) Spring and Summer (April X 

September) Sampling Events. 

Cyanobacteria Greens Diatoms Cryptophytes Dinoflagellates Other

Fresh 31.1 2.9 57.5 3.6 4.3 0.7

Marine 11.6 1.1 77.2 3.8 5.9 0.3

St. Johns River Water Management District 31
Figure 22. Change in Phytoplankton Community Richness from Freshwater to Marine 

Stations in the LSJR. 

Relative Species Richness x Salinity

0

10

20

30

40

50

60

70

80

90

100

6.00 6.50 7.00 7.50 8.00 8.50 9.00 9.50 10.00 10.50

Ln(Salinity x 1000)

Relative Spp. Richness, %

2001

1999

4 to 16 ppt

Figure 23. Mean Number of Phytoplankton Species within the Top 10 based on 

Biovolume, at a Given Station, Present in the Next Downstream Station as a Function of 

the Mean Salinity Between the Two Stations. Data are for 1999 and 2001 (Phlips and 

Cichra, 2001). 

Phytoplankton Community Continuity

0

1

2

3

4

5

6

7

123 4567

Salinity Range

Species in Com

mon Between 

Stations

I:\\esdata\l sj \ UF-Pl anktonI D\Phyto-T axa\Salini tySt. Johns River Water Management District 32
condition of a predominantly marine bloom was assumed to apply when chloride 

concentrations were greater than 1,500 mg/L (roughly equivalent to 2.7 psu), consistent 

with the definition of Cpredominantly marineD water in the F.A.C. 62-302. 

 

Plankton and water quality data from five ambient monitoring stations have been 

examined extensively to describe the patterns of algal growth within this reach. These

stations, shown in Figure 21, are Mandarin Point, Piney Point, Talleyrand, Fulton Point 

and Plummers Cove (a short term monitoring station). With the exception of Plummers , 

all stations are located at the riverPs mid-channel. There is some indication that this

center channel approach to plankton monitoring may lead to an under-reporting of the 

amount of algal biomass within this reach. Observational and anecdotal information 

indicates that algal blooms more frequently reach nuisance levels in near shore areas.

The possibility of higher algal biomass near shore, due to factors such as positive

buoyancy compensation, salinity-induced aggregation and subsequent wind-stacking of 

Microcystis (Sellner et al., 1988), dense growth of filamentous green alga on SAV 

(Magley W unpublished data), or longer near-shore water entrainment (Dobberfuhl, pers. 

comm.) are plausible. In a demonstration of the potential for near shore or cove locations 

to exhibit higher algal biomass levels than channel stations, paired, same-day sample data 

from two near-by stations at Mandarin Point, one in the channel and the other in 

Plummers Cove, were compared from the time period from December 1996 through 

October 1999. The in-cove station was found to have a significantly higher mean 

chlorophyll a concentration (two-tailed paired t-test, p=0.05), with an average increase of 

3.2 mg/m3

. The in-cove station exceeded the channel station by more than 10 mg/m3 on 

3 of the 34 paired events, while the channel station never exceeded the cove station by 

more than 6 mg/m3. Thus there is reason to suspect that algal biomass, as estimated by

centerline sampling stations, may underestimate the area-weighted condition. 

Annual patterns of chlorophyll a and algal biovolume for the years from 1998 through 

2001 are shown in Figures 24 and 25 for the four river channel stations. Both of these 

algal biomass indicators are shown, as neither appears to be a superior measure in this 

St. Johns River Water Management District 33
Figure 24 . Total Chlorophyll a Concentrations for Oligo/Mesohaline Stations in the 

LSJR, 1998 C 2001. 

(a) 1998

0

10

20

30

40

50

60

70

1/1 1/31 3/3 4/2 5/3 6/2 7/3 8/2 9/2 10/2 11/2 12/2 1/2

Total Chlorophyll-a, mg/m 3

Fulton Pt.

Talleyrand

Piney Point

Mandarin Pt.

(b) 1999

0

10

20

30

40

50

60

70

1/1 1/31 3/3 4/2 5/3 6/2 7/3 8/2 9/2 10/2 11/2 12/2 1/2

Total Chlorophyll-a, mg/m 3

Fulton

Talleyrand

Piney Pt.

Mandarin

St. Johns River Water Management District 34
Figure 24 (cont.). Total Chlorophyll a Concentrations for Oligo/Mesohaline Stations in 

the LSJR, 1998 E 2001. 

( c ) 2000

0

10

20

30

40

50

60

70

1/1 1/31 3/2 4/1 5/2 6/1 7/2 8/1 9/1 10/1 11/1 12/1

Total Chlorophyll-a, mg/m 3

Fulton

Talleyrand

Piney Pt.

Mandarin

(d) 2001

0

10

20

30

40

50

60

70

1/1 1/31 3/3 4/2 5/3 6/2 7/3 8/2 9/2 10/2 11/2 12/2 1/2

Total Chlorophyll-a, mg/m 3

Fulton

Talleyrand

Piney Pt.

Mandarin

St. Johns River Water Management District 35
Figure 25. Total Algal Biovolume for Oligo/Mesohaline Stations in the LSJR, 1998 C 

2001. From Phlips and Cichra, 2000. 

(a) 1998

0

2000

4000

6000

8000

10000

12000

1/1 1/31 3/3 4/2 5/3 6/2 7/3 8/2 9/2 10/2 11/2 12/2 1/2

Total Biovolume, micro-m 3/ml*1000

Fulton Pt.

Talleyrand

Piney Point

Mandarin Pt.

(b) 1999

0

2000

4000

6000

8000

10000

12000

1/1 1/31 3/3 4/2 5/3 6/2 7/3 8/2 9/2 10/2 11/2 12/2 1/2

Total Biovolume, micro-m 3/ml*1000

Fulton

Talleyrand

Piney Pt.

Mandarin

St. Johns River Water Management District 36
Figure 25 (cont.). Total Algal Biovolume for Oligo/Mesohaline Stations in the LSJR, 

1998 F 2001. From Phlips and Cichra, 2000. 

( c ) 2000

0

2000

4000

6000

8000

10000

12000

1/1 1/31 3/2 4/1 5/2 6/1 7/2 8/1 9/1 10/1 11/1 12/1

Total Biovolume, micro-m 3/ml*1000

Fulton

Talleyrand

Piney Pt.

Mandarin

(d) 2001

0

2000

4000

6000

8000

10000

12000

1/1 1/31 3/3 4/2 5/3 6/2 7/3 8/2 9/2 10/2 11/2 12/2 1/2

Total Biovolume, micro-m3/ml*1000

Fulton

Talleyrand

Piney Pt.

Mandarin

St. Johns River Water Management District 37
river reach. While chlorophyll a should be a better indicator of productivity potential, 

because it is a less dominant photosynthetic pigment in the marine phytoplankton 

community, it may not provide as reliable an indicator of algal biomass. Biovolume

measurements might be expected to provide a better indication of biomass here, but can 

be difficult due to the high amount of tripton and possibility for empty diatom frustules 

appearing to be live cells. Both measures consistently predict the high biomass 

associated with the import of the freshwater bloom in August of 1998, but do not 

correlate well otherwise. Unlike the freshwater LSJR, where chlorophyll a concentration 

was found to be a reliable indicator of algal biomass, and linear regressions between 

particulate organic carbon and chlorophyll a, and between algal biovolume and 

chlorophyll a, produced high R2

 values, similar comparisons in this reach were poor The

boundary relationships between POC and the POC:chlorophyll a ratio and between POC 

and the POC:total biovolume ratio (Figure 26a and b) suggests the presence of a much 

larger amount of non-algal POC for marine samples. This is not a surprising result for

the low salinity region of a river estuary such as the LSJR, as the delivery of 

allochthonous and autochthonous organic matter, and the possible flocculation of 

dissolved organic matter, likely contribute greatly to the POC pool. Boundary 

relationships can be discerned, however, and when the lower bounds of these scatter plots 

are compared to the freshwater algal carbon to chlorophyll a and biovolume, conversions 

developed for LSJR freshwater algal communities do not appear to be inconsistent for 

marine communities, and therefore have been used when conversions to algal carbon are 

required. 

With the exception of the peak biovolume observed in 1998 at the Mandarin and Piney 

Pt. Stations, all summer sampling events in this reach were characterized by 

predominantly marine conditions and were assumed representative of estuarine 

phytoplankton communities. For low-flow years, peak biovolume measurements tended 

to range between 2,000,000 to 4,000,000 Pm3

/ml, with large blooms of over 9,000,000 

Pm3/ml occurring at Mandarin Point in July 2000 and Fulton Point in June 2001. In 

recent work on the Indian River Lagoon, Phlips et al. (2003) identified a biovolume level 

St. Johns River Water Management District 38
Figure 26. Calculated organic carbon to biovolume conversion for predominantly marine 

blooms of the Lower St. Johns River. Based on 186 measurements from August 1998 

through November 2001. Red line indicate carbon to biomass relationships based on 

freshwater phytoplankton in the LSJR. Dashed pink line of (a) represents calculated 

reduction in carbon to biomass ratio corresponding to the proportional loss from silica in 

diatoms. 

(a) Marine POC:Biovolume Ratio

0

2000

4000

6000

8000

10000

12000

0 0.001 0.002 0.003 0.004

POC:Biovolume

Total Biovolume, microm3/mlx1000

Observed Data

Freshwater C:Biov Ratio

Silica-Adjusted Ratio

(b) Marine Carbon:Chlorophyll-a

0

5

10

15

20

25

30

35

40

45

50

0 100 200 300 400 500 600 700 800

POC:Chlorophyll-a

Chlorophyll-a, mg/m3

Observed Data

50:1 C:Chlorophyll-a

St. Johns River Water Management District 39
of 1,000,000 Pm3

/ml (roughly equivalent 6 μg/L chlorophyll a) as indicative of a marine 

bloom condition. 

Peak chlorophyll a concentrations ranged between 10 and 40 mg/m3

. With the exception 

of the very high value at Mandarin in July 2000, biovolume tended to be slightly higher 

at downstream stations Talleyrand and Fulton Point. When sampling events were 

performed for both high and low tides in the same day at Fulton Point, it was observed 

that higher chlorophyll and algal biovolume tended to occur on high tide sampling, 

despite lower nutrient concentrations. High tide collections at this location, due to its 

close proximity to the riverNs mouth, are assumed to be largely representative of the near 

coastal plankton community. Due to less vertical mixing and greater transparency, the 

near coastal area at the St. Johns mouth may support conditions more favorable for 

growth, as has been observed for the near coastal area offshore of Georgia (Yoder et al., 

1993), and thus river nutrients can be exploited by marine phytoplankton. 

While increases in spring-summer biomass appear to be less pronounced than that 

observed for the freshwater reach, the relative magnitudes of biomass increase are only

marginally less. Mean oligo/mesohaline April V September chlorophyll a from 1997 

through 2001 was 11.4 mg/m3

, a 75% increase over the October V March mean of 6.5 

mg/m3

. In comparison, freshwater mean April V September chlorophyll a mean of 34.4 

mg/m3

 represents a 95% increase over the October V March concentration of 17.6 mg/m3. 

Nutrient Limitations to Marine Phytoplankton Community Growth 

The amount of bioavailable silica may be a key regulator in the diatom bloom expansion 

potential within the LSJR marine reach. Low silica concentrations co-occur with peak 

diatom biomass (Figure 27). The occurrence of low concentrations of essential inorganic

nutrients, in the range of reported half saturation constant concentrations, can be a useful

indicator of potential nutrient limitation. This technique is more difficult to apply with 

confidence in this instance due to the method detection limit for silica analyses being

over 10 times greater than the commonly reported half saturation concentration range of 

St. Johns River Water Management District 40
Figure 27. Relationship between silica concentrations and diatom biovolume. Data from

1997 through 2001 for predominantly marine condition (>2.7 ppt) samples. 

Relationship Between Dissolved Silica Concentration and

Diatom Biovolume

0

2000

4000

6000

8000

10000

12000

0 1 2 3 4 5

Dissolved Si, mg/L

Diatom Biovolume, micro-m3/1000

6

Relationship Betw. Monthly Mean Diatom Biovolume and 

Percent of Dissolved Si Analyses Below the MDL

0

10

20

30

40

50

60

70

80

90

100

0 200 400 600 800 1000 1200 1400 1600 1800 2000

Mean Monthly Diatom Biovolume, micro-m3/1000

Percent Diss. Si Below MDL

St. Johns River Water Management District 41
20 - 100 μg/L (EPA, 1990; Chapra, 1997). In the data set used here, @best estimatedD 

concentrations below the MDL, rather than censored values, are reported, and peak 

diatom biovolumes appear to be associated with low, even potentially limiting, dissolved 

silica concentrations. However, due to the low confidence attributed to these belowMDL values, the derivation of a quantitative relationship has not been attempted. 

Prevailing low silica concentrations appears to be a natural characteristic in many of 

FloridaRs surface waters, presumably due to watershed parent material predominated by

sands resistant to weathering, and the general absence of lattice clays that are rich in 

bioavailable silica. In the LSJR marine reach, the upper boundary of the silica to diatom 

biovolume relationship suggests that diatom biomass within the river may become

generally limited by silica in the range of 3 to 4 million μm3

/ml (Figure 27). 

Low bioavailable silica may play an important role in shaping phytoplankton 

communities when other macro-nutrients, primarily N and P, are in sufficient supply to

promote silica limitation. The bar chart of Figure 28 shows the relationship between 

dinoflagellate relative abundance and the potential severity of silica limitation, based 

upon dissolved silica concentration. While the confidence intervals in Figure 28 overlap 

for the two lowest concentration classes, the removal of one sample event that occurred 

during the El Nino year (1998) early summer results in significant difference between 

these two groups at a level of p = 0.10. This suggests that when silica concentration is 

very low and possibly limiting to diatom growth, other algal species, primarily 

dinoflagellates, are able to take advantage of excess bioavailable N and P and reduced 

competition to increase their abundance. Turner (2002), in a recent article on the 

influence of nutrient ratios in shaping plankton food webs, cites 10 nutrient manipulation 

studies performed in mesocosms in estuarine environments that strongly support the 

concept of flagellate growth being positively advantaged by increases in nitrogen and 

phosphorus relative to silica. Turner (2002) suggests a ratio of bioavailable Si:N of <1 

represents a sensitive pivot point at which diatom species tend to decline relative to 

flagellate species. 

St. Johns River Water Management District 42
Figure 28. Mean relative abundance of dinoflagellates biovolume within silica 

concentration classes. Error bars encompass 90% confidence interval. 

Dinoflagellate Relative Abundance within Silica

Concentration Classes

0.0

2.0

4.0

6.0

8.0

10.0

12.0

14.0

16.0

18.0

0 - 0.25 0.25 - 0.5 0.5 - 1.0 > 1.0

Si Concentration Class

Mean Relative Abundance

St. Johns River Water Management District 43
Table 4. Dinoflagellate Species Occurring in the Oligo/Mesohaline LSJR for Blooms with Dinoflagellate Biovolume > 300,000 

μm3/ml.

Dinoflagellate Species Composition for Blooms with Biovolume >= 300. Mean Relative abundance = 37%. Biovolume Genus/Species Biovolume Genus/Species Biovolume Genus/Species

Fulton Pt. Surface 3/31/1998 Fulton Pt. Bottom 3/31/1998 Mandarin Pt. 9/22/1998

6208Unidentified armored dinoflagellates > 25m 4656Unidentified armored dinoflagellates > 25m 17480Gymnodinium < 30m6829Unidentified armored dinoflagellates < 25m 7152Ceratium hircus 284778Division Pyrrhophyta armored < 25m

421Katodinium 2894Gymnodinium < 30m 

2659Prorocentrum 471393Gymnodinium 

12042Prorocentrum maximum 6912Prorocentrum 

1564Dinophysis caudata 41791Prorocentrum maximum 

1263Oxyphysis 

Plummers Cove 5/27/1999 Fulton Pt. Surface 8/31/1999 Fulton Pt. Bottom 8/31/1999

15278Unidentified armored dinoflagellates > 25m 278098Unidentified armored dinoflagellates > 25m 128010Unidentified armored dinoflagellates > 25m

4223Unidentified armored dinoflagellates > 25m 3016Ceratium 2171Gymnodinium < 30m

17480Gymnodinium < 30m 724Gymnodinium < 30m 2490Gyrodinium 

386937Prorocentrum minimum 2171Gymnodinium < 30m 3446Gyrodinium 

31426Gymnodinium 323Gyrodinium minimum 

5041Gymnodinium 3090Gyrodinium micans 7340Gyrodinium micans 4785Gyrodinium 1607Gyrodinium 1564Dinophysis caudata 6027Gonyaulax 3013Gonyaulax 

St. Johns River Water Management District 44
Table 4. (cont.) 

Biovolume Genus/Species Biovolume Genus/Species Biovolume Genus/Species

Fulton Pt. Surface 9/29/1999 Fulton Pt. Bottom 9/29/1999

5174Unidentified armored dinoflagellates > 25m 21812Unidentified armored dinoflagellates > 25m3576Ceratium hircus 10729Ceratium hircus 

2521Gymnodinium < 30m 276076Gymnodinium < 30m

2490Gyrodinium 2490Gyrodinium 

803Prorocentrum 5022Prorocentrum micans 

3013Gonyaulax 6026Prorocentrum 

3127Dinophysis caudata 

1482?

421Oxyphysis 

5091?

Mandarin Pt. 6/27/2000 Fulton Pt. 6/27/2000 Mandarin Pt. 7/25/2000

442989Unidentified armored dinoflagellates > 25m 406896Unidentified armored dinoflagellates > 25m 24770Unidentified armored dinoflagellates > 25m

52439Gymnodinium < 30m 64305Gymnodinium < 30m 219812Gymnodinium < 30m

28320Katodinium 22608Gymnodinium

161Prorocentrum minimum 

Talleyrand Surface 11/2/2000 Talleyrand Bottom 11/2/2000 Fulton Pt. 6/26/2001 

6871Unidentified armored dinoflagellates > 25m 436141Unidentified armored dinoflagellates > 25m 848496Unidentified armored dinoflagellates > 25m

1672Gymnodinium < 30m 5532Gymnodinium < 30m 3713?

161Prorocentrum minimum 5238Gymnodinium 7548Ceratium tripos 

1066Katodinium 2605Gymnodinium < 30m

5179? 94Prorocentrum micans 

2300Gonyaulax 

St. Johns River Water Management District 45
The principle dinoflagellate species or genera that are seen to occur at time of high 

dinoflagellate biomass are summarized in Table 4. Among these dinoflagellates are a 

number of species with known toxin production capability, thus, the reduction in the 

abundance of dinoflagellates presents itself as a potentially important restoration 

objective for nutrient management in the LSJR. Doctors Lake, located near Mandarin 

Point along the riverGs western shore, provides an extreme example of how flowrestricted coves and embayments, under predominantly oligo- to mesohaline conditions

(a condition under which, it is important to note, the lake has been fed mainly be river 

waters), can manifest conditions of nutrient enrichment into serious blooms of potentially 

toxic dinoflagellate species. Doctors Lake is heavily used for recreational purposes, is 

surrounded by dense residential development, and is extensively fished for shrimp and 

crab. In the 18 sampling events performed within the lake between 1997 and 2001 in 

which predominantly marine conditions prevailed, 7 of these had dinoflagellate 

biovolumes in excess of 300,000 μm3

/ml, and 5 events exhibited dinoflagellate 

biovolumes in excess of 1,000,000 μm3

/ml. In 2 of these 5 events, a species of 

Gymnodinium was the dominant phytoplankton, and the dominant dinoflagellate in one 

more. In one of the 5 events, Prorocentrum minimum was the dominant phytoplankton, 

with a biovolume alone of over 1,500,000 μm3

/ml. 

The presence and patterns in bioavailable N and P can be an important indicator of 

potential nutrient limitation in the phytoplankton community. High concentrations of 

bioavailable nutrients, in excess of the requirements for algal growth, can indicate that 

large nutrient reductions may be necessary in order to bring nutrients into the growthlimiting range. High concentrations also pose the risk of large, detrimental blooms

should the proper set of hydrodynamic and meteorological conditions prevail.

Bioavailable nutrients are generally more abundant in the oligo/mesohaline reach of the 

river, owing to the proximity of urban area external load and the remineralization of algal 

nutrients from the salinity-stressed freshwater community. 

Hydrodynamic and river morphologic factors relevant to algal biomass accrual are 

dramatically different in the oligo/mesohaline reach when compared to the upstream, 

St. Johns River Water Management District 46
freshwater zone. Increased channel depth, particularly in the mesohaline reach, decreases 

the proportion of river volume within the photic zone, and acts to lower per area 

production rates. In addition, tidal exchange within the dredged river mouth is very 

large, resulting in water volume exchange rates from Piney Point onward of less than 10 

days (Sucsy, pers. comm.). Thus, despite the large influx of external load N and P, and 

abundant within-river nutrient concentrations, hydrodynamic exchange can offset rates of 

bloom expansion. Hydrodynamic mixing may also move blooms out of the photic zone, 

contributing to dissolved oxygen depression and worsening the negative water quality 

impacts when blooms do occur. 

Cumulative frequency distributions of total inorganic nitrogen and soluble reactive 

phosphorus for sampling performed under marine conditions within the oligohaline and 

mesohaline reach are shown in Figure 29, and from these it can be seen that low or near

limiting concentrations are seldom observed. For sampling performed between 1998 and 

2001, inorganic nitrogen concentrations were only seen at potentially limiting levels in 

14% of the 188 sample collections, and orthophosphate only at 3.5%. Figures 30 and 31 

present time series data for inorganic nutrients (total inorganic N (TIN) and 

orthophosphate (PO4)) for the most downstream plankton and water quality monitoring 

station at Fulton Point, to demonstrate these patterns in potential N and P competition. 

For the Fulton Point station in 1997 and 1998, TIN is for the most part above 

concentrations believed to be limiting to growth. In the dry years of 1999 and 2000, the 

potential for nitrogen limitation appears greater, in particular for incoming (high) tide

samples. In years when high and low tide sample data are available, high tide events 

exhibit lower concentrations of TIN. This is believed to be due to dilution by low 

concentration oceanic waters, as well as greater competition for nutrients in the near 

coastal zone at the rivers mouth, where algal biomass is often greater. A similar pattern

occurs for orthophosphate (Figure 31); however, concentrations of dissolved total 

phosphorus (Figure 32) are high at this station, so the possibility of phosphorus limitation 

in the phytoplankton is seems less likely. Verity et al. (1992) also observed limiting 

concentrations of inorganic nitrogen, relative to silica and orthophosphate, in South 

Atlantic Bight near coastal waters. 

St. Johns River Water Management District 47
Figure 29. Cumulative frequency distribution of inorganic N and P for the LSJR near 

Piney Point, 1998 D 2001. 

(a) Total Inorganic N

0

10

20

30

40

50

60

70

80

90

100

0 1 2 3 4 5 6 7

Ln(TIN, mg/m3)

Percent Frequency

Doctors Lake

Fulton Pt.

Talleyrand

Piney Pt.

Mandarin Pt.

20 mg/m3

(b) Soluble Reactive P

0

10

20

30

40

50

60

70

80

90

100

0 1 234 5 6

Ln(TIN, mg/m3

)

Percent Frequency

Doctors Lake

Fulton Pt.

Talleyrand

Piney Pt.

Mandarin Pt.

5 mg/m3

St. Johns River Water Management District 48
Figure 30. Time series plots of total inorganic nitrogen concentration for the LSJR near 

Fulton Point, 1997 @ 2000. Total inorganic nitrogen calculated as the sum of total NH4 + 

NOX. Evolution in monitoring programs results in changing levels of vertical and tidal 

distinction in sampling data from year to year. Pink dashed line corresponds to 0.02 

mg/L, a concentration at which nitrogen is assumed to be potentially limiting to growth. 

a. 1997

0

0.1

0.2

0.3

0.4

0.5

0.6

1/1 1/31 3/2 4/2 5/2 6/2 7/2 8/1 9/1 10/1 11/1 12/1

TIN, mg/L

Top

b. 1998

0

0.1

0.2

0.3

0.4

0.5

0.6

1/31 3/2 4/1 5/2 6/1 7/2 8/1 8/31 10/1 10/31 12/1 12/31 1/30

TIN, mg/L

Top - High

Top - Low

St. Johns River Water Management District 49
Figure 30 (cont.). Time series plots of total inorganic nitrogen concentration for the LSJR 

near Fulton Point, 1997 B 2000. Total inorganic nitrogen calculated as the sum of total 

NH4 + NOX. Evolution in monitoring programs results in changing levels of vertical and 

tidal distinction in sampling data from year to year. 

c. 1999

0

0.1

0.2

0.3

0.4

0.5

0.6

1/1 1/31 3/2 4/2 5/2 6/2 7/2 8/1 9/1 10/1 11/1 12/1 12/31

TIN, mg/L

Bottom - High

Bottom - Low

Mid - High

Mid - Low

Top - High

Top - Low

d. 2000

0

0.1

0.2

0.3

0.4

0.5

0.6

12/31 1/30 2/29 3/31 4/30 5/31 6/30 7/30 8/30 9/29 10/30 11/29

TIN, mg/L

Bottom - High

Bottom - Low

Mid - High

Mid - Low

Top - High

Top - Low

St. Johns River Water Management District 50
Figure 31. Time series plots of orthophosphate concentration for the LSJR near Fulton 

Point, 1997 ? 2000. Evolution in monitoring programs results in changing levels of 

vertical and tidal distinction in sampling data from year to year. Pink dashed line 

corresponds to 0.005 mg/L, a concentration at which phosphorus is assumed to be 

potentially limiting to growth. 

a. 1997

0

0.02

0.04

0.06

0.08

0.1

1/1 1/31 3/2 4/2 5/2 6/2 7/2 8/1 9/1 10/1 11/1 12/1

Orthophosphate, mg/L

Top

b. 1998

0

0.02

0.04

0.06

0.08

0.1

1/31 3/2 4/1 5/2 6/1 7/2 8/1 8/31 10/1 10/31 12/1 12/31 1/30

Orthophosphate, mg/L

Top - High

Top - Low

St. Johns River Water Management District 51
Figure 31 (cont.). Time series plots of orthophosphate concentration for the LSJR near

Fulton Point, 1997 A 2000. Evolution in monitoring programs results in changing levels 

of vertical and tidal distinction in sampling data from year to year. Pink dashed line 

corresponds to 0.005 mg/L, a concentration at which phosphorus is assumed to be 

potentially limiting to growth. 

c. 1999

0

0.02

0.04

0.06

0.08

0.1

1/1 1/31 3/2 4/2 5/2 6/2 7/2 8/1 9/1 10/1 11/1 12/1 12/31

Orthophosphate, mg/L

Bottom - High

Bottom - Low

Mid - High

Mid - Low

Top - High

Top - Low

d. 2000

0

0.02

0.04

0.06

0.08

0.1

12/31 1/30 2/29 3/31 4/30 5/31 6/30 7/30 8/30 9/29 10/30 11/29

Orthophosphate, mg/L

Bottom - High

Bottom - Low

Mid - High

Mid - Low

Top - High

Top - Low

St. Johns River Water Management District 52
Figure 32. Total dissolved P at Fulton Point, 1997 9 2001. 

a. 1997

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

12/31/96 3/2/97 5/2/97 7/2/97 9/1/97 11/1/97

Total Dissolved P, m

g/L

Top

b. 1998

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

2/4/98 3/26/98 5/15/98 7/4/98 8/23/98 10/12/98 12/1/98 1/20/99

Total Dissolved P, mg/L

Top - High

Top - Low

St. Johns River Water Management District 53
Figure 32 (cont.). Total dissolved P at Fulton Point, 1997 < 2001. 

c. 1999

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

12/31/98 3/1/99 4/30/99 6/29/99 8/28/99 10/27/99 12/26/99

Total Dissolved P, m

g/L

Bottom - High

Bottom - Low

Mid - High

Mid - Low

Top - High

Top - Low

d. 2000

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

12/26/99 2/25/00 4/26/00 6/26/00 8/26/00 10/26/00

Total Dissolved P, mg/L

Bottom - High

Bottom - Low

Mid - High

Mid - Low

Top - High

Top - Low

St. Johns River Water Management District 54
Patterns in Oxygen Deficits 

Persistent, low concentrations of dissolved oxygen in the meso/polyhaline reach of the 

LSJR are a well documented but poorly understood phenomena. First studied intensively 

in the 1950Es, these occurrences were attributed to the discharge of untreated domestic 

sewage and industrial waste (Pyatt, 1964). Despite large improvements in point source 

treatment, the occurrence and severity of these episodes has remained unchanged over 

time (Figure 32). Intensification of monitoring of dissolved oxygen since 1996, the 

comprehensive examination of external load sources, and the current level of 

understanding of the manifestations of nutrient loading and estuarine eutrophication have 

now helped to clarify our understanding of these events. 

To better describe the short-term fluctuation in dissolved oxygen associated with tide 

stage, diurnal photosynthesis patterns and intermittent reverse flows, the U.S. Geological 

Survey established a series of continuous, automated dissolved oxygen stations in the 

fresh and marine reaches of the LSJR (see maps Figures 2 and 21). Stations are 

instrumented with temperature, salinity and dissolved oxygen sensors and configured to 

collect at two to three vertical positions at hourly intervals. The daily average dissolved 

oxygen data from the monitoring stations at Dames Point and the Acosta Bridge are 

shown in Figure 33. From the annual time series plots of Figure 33, annual minimum 

dissolved oxygen concentrations can be seen to occur between July and September, 

coincident with the annual maximum temperatures and minimum oxygen saturation 

concentrations. 

Lower levels of dissolved oxygen are consistently seen at the Dames Point station. For

the 21⁄2-year record at Dames Point from early 1996 through September 1999, oxygen 

concentrations were below 5 mg/L 15 percent of the time at the surface and 35 percent of 

the time in the near-bottom water (Figure 35). Over the same time period, the gauge at 

Acosta Bridge exhibited below 5 mg/L oxygen concentrations only 1⁄2 percent of the time

at the surface and 4 percent of the time in near-bottom water. Extreme low dissolved 

oxygen levels (< 2 mg/L) occur rarely, with the 1 percentile daily mean concentration for 

St. Johns River Water Management District 55
Figure 33. Comparison with historic (1961-65) measurements shows no change in mean 

monthly dissolved oxygen levels 

LSJR at Jacksonville

2

3

4

5

6

7

8

9

10

Feb. Apr. Jun. Aug. Oct. Dec.

Mean Monthly D.O., mg/L

Main St., 1961-65

Acosta Br., 1996-01

Dames Pt., 1996-01

St. Johns River Water Management District 56
Figure 34. Mean daily dissolved oxygen concentrations measured at USGS automated 

monitoring stations at Acosta Bridge and Dames Point, Mid-depth, 1996 through 2001. 

Lines with symbols are the observed data. Finer, solid un-symboled lines are the oxygen 

concentrations for based on mean daily mid-depth salinity and temperature. Horizontal 

red line corresponds to the water quality standard of 5 mg/L daily mean of F.A.C. 62-302. 

(a) 1996

2

3

4

5

6

7

8

9

10

11

1/1/1996 3/1/1996 4/30/1996 6/29/1996 8/28/1996 10/27/1996 12/26/1996

mg/L

Dames Pt.

Acosta Br.

(b) 1997

2

3

4

5

6

7

8

9

10

11

12/31/1996 3/1/1997 4/30/1997 6/29/1997 8/28/1997 10/27/1997 12/26/1997

mg/L

Dames Pt Measured.

Acosta Br. Measured

St. Johns River Water Management District 57
Figure 34 (cont.). Mean daily mid-depth dissolved oxygen concentrations measured at 

USGS automated monitoring stations at Acosta Bridge and Dames Point, 1996-2001. 

(c) 1998

2

3

4

5

6

7

8

9

10

11

12

12/31/1997 3/1/1998 4/30/1998 6/29/1998 8/28/1998 10/27/1998 12/26/1998

mg/L

Dames Pt.

Acosta Br.

(d) 1999

2

4

6

8

10

12

14

12/31/1998 3/1/1999 4/30/1999 6/29/1999 8/28/1999 10/27/1999 12/26/1999

mg/L

Dames Pt.

Acosta Br.

St. Johns River Water Management District 58
Figure 34 (cont.). Mean daily mid-depth dissolved oxygen concentrations measured at 

USGS automated monitoring stations at Acosta Bridge and Dames Point, 1996-2001. 

(e) 2000

2

3

4

5

6

7

8

9

10

11

12

12/31/1999 2/29/2000 4/29/2000 6/28/2000 8/27/2000 10/26/2000 12/25/2000

Dissolved Oxygen, m

g/L

Dames Pt.

Acosta Br.

(f) 2001

2

3

4

5

6

7

8

9

10

11

12

12/30/2000 2/28/2001 4/29/2001 6/28/2001 8/27/2001 10/26/2001 12/25/2001

Dissolved Oxygen, m

g/L

Dames Pt.

Acosta Br.

St. Johns River Water Management District 59
Figure 35. Cumulative frequency distributions of mean daily dissolved oxygen for USGS 

automated stations at Acosta Br. and Dames Point. 

Acosta Daily Dissolved Oxygen Frequency Distribution

0

10

20

30

40

50

60

70

80

90

100

2 3 4 5 6 7 8 9 10 11 12

Concentration, mg/L D.O.

Cumulative Frequency

Surface

Middle

Bottom

Dames Pt. Daily Dissolved Oxygen Frequency Distribution

0

10

20

30

40

50

60

70

80

90

100

234 5678 9 10

Concentration, mg/L D.O.

Cumulative Frequency

Surface

Middle

Bottom

St. Johns River Water Management District 60
Dames Point being 3.8 mg/L. Vertical oxygen stratification is not strongly exhibited, 

with the mean difference between surface and mid sensors, and between mid and bottom

sensors at Dames Point being 0.34 mg/L and 0.30 mg/L, and at Acosta being 0.26 mg/L 

and 0.17 mg/L. The longitudinal pattern in dissolved oxygen concentration is stronger 

than the vertical (Figure 35(a)), and tends to exhibit an oxygen minimum zone between 

river mile 15 (10 miles upstream of the mouth) and river mile 20. 

Examination of oxygen saturation deficit (oxygen saturation deficit = saturation 

concentration P observed concentration) allows for the comparison of oxygen demand 

without the effect of salinity and temperature. The difference between oxygen saturation 

deficit at Acosta Bridge and Dames Point is significant, but examination of the 

distribution of saturation deficit (Figure 36) reveals that the difference is due to the 

tendency for lower values (i.e., greater instances of near saturation or even supersaturation) to occur at the Acosta Bridge site. The intensity of severe saturation deficit is

similar for both locations, indicating that the lower oxygen levels at Dames Point are 

largely due to greater salinity. 

The amount of algal biomass present, and the rate of expansion or contraction in the 

phytoplankton community, is significantly correlated to the general level of oxygen 

saturation deficit. The degree of this control is demonstrated in Figure 37, which 

compares the rate of change in chlorophyll a between sampling dates to the oxygen

deficit observed for these events. Expansion in the algal community can be seen to be 

significantly, negatively correlated with the oxygen saturation deficit existing on a given 

sampling day, while contraction in the community is associated with increases in 

saturation deficit. The per unit change in oxygen saturation deficit for a given amount of 

chlorophyll a change between consecutive sampling events is not significantly different 

between Acosta Bridge and Dames Point (i.e., slopes and intercepts not significantly 

different). Large, positive changes in chlorophyll a are not typically seen at the Dames 

Point station, and this is consistent with the lack of conditions of oxygen super-saturation 

measured at this location. The intercept of this relationship, 1.54 mg/L oxygen 

St. Johns River Water Management District 61
Figure 36. Longitudinal dissolved oxygen saturation pattern in the Meso/Polyhaline 

LSJR. Data are from Summer 1997 ambient monitoring programs. 

(a) Oxygen Concentration

4.5

5

5.5

6

6.5

7

7.5

0 5 10 15 20 25 30 35

River Mile

Mean Dissolved Oxygen, 

mg/L

(b) Percent Saturation

70

75

80

85

90

95

100

0 5 10 15 20 25 30 35

River Mile

Mean Oxygen % Saturation

St. Johns River Water Management District 62
Figure 37. Distribution of daily mean oxygen saturation deficit for Acosta Bridge and 

Dames Point in the LSJR near Jacksonville. 

Oxygen Saturation Deficit = Saturation - Observed

0

10

20

30

40

50

60

70

80

90

100

-2 -1 0 1234

Saturation Deficit, mg/L

% of Time Greater

Dames Point

Acosta Br.

Figure 38. Relationship between the Direction and Magnitude of Change in Chlorophyll 

a and the Sampling Day Oxygen Saturation Deficit at Dames Point and Acosta Bridge. 

Chlorophyll a change rate determined as the difference between sampling dates/time 

interval for water masses of equal salinity. Water mass equal salinity chlorophyll a

concentration determined by interpolation between bracketing salinities. Regression line

determined for complete data set; individual regression lines not significantly different. 

Determinations made for June M September sampling dates from 1996 through 2000, with 

the exception of 1999, when October and early November data were included to include 

an event of significant oxygen supersaturation. 

St. Johns River Water Management District 63

-2

-1.5

-1

-0.5

0

0.5

1

1.5

2

2.5

3

3.5

-2 -1 0 1 2 3

Daily Rate of Chlorophyll a Change, mg/m3

/day

Sampling Day Oxygen Saturation 

Deficit, mg/L

Acosta Br.

Dames Point

O2 Saturation Def. = -0.97*(Chl-a 

Change Rate) + 1.54

Saturation Deficit

Supersaturation
saturation deficit, is interesting and suggests that the St. Johns River in this reach tends to 

maintain a background level of respiration in excess of production. 

The overall relationship of Figure 37 suggests that over two thirds (R2

 = 0.68) of the 

variation in oxygen saturation deficit can be accounted for by changes in the algal 

community. The short-term changes in oxygen saturation deficit were also compared to 

the occurrence of rainfall and stormwater runoff events. While on some occasions, 

oxygen saturation deficit does appear to increase in days following storm events, this 

effect is not consistent, and could not be distinguished from other cyclic factors (such as

tide reversals) or secondary effects on the phytoplankton community (such as temporary 

turbidity or color increases that might reduce the photosynthesis/respiration ratio). 

The prevailing salinity regime in the narrow, Jacksonville reach of the LSJR (the 25th and

75th percentile values of daily mean salinity at Dames Point from May 1996 through 

September 2001 were 20.3 and 27.6 psu), and the longitudinal trend in phytoplankton 

community composition changes (as shown in Figures 22 (a) and (b); maximum 

community composition change occurring between 18 and 25 psu) leads to the 

conclusion that this reach of the river is frequently the location of relatively sharp

transitions in the algal community. Expected with the decline of out-flowing, fresh and 

oligohaline phytoplankton communities, or inflowing marine communities, would be 

increased algal respiration, senescence, and decomposition, leading to increases in

oxygen deficit. In addition, the narrower and more turbulent channel in this reach

translates to a reduction of the cross-sectional area of photic zone and an overwhelming 

of light-enhancing vertical migration adaptations in the algae. It should therefore be 

expected that as algal biomass increases, rates of algal community decline will increase,

as will associated oxygen deficits in this river zone. 

In summary, salt-tolerant and marine algal communities present from the riverXs 

oligohaline front to the mouth appear capable of exploiting nutrient loads, at times

leading to adverse water quality conditions. As has been commonly documented for

other eutrophic estuaries, augmented algal growth in the LSJR ultimately manifests in 

St. Johns River Water Management District 64
lowered dissolved oxygen, and levels below the state standard of 5 mg/L daily average or 

4 mg/L instantaneous value are commonly observed during summer and early fall. The 

degree of nutrient exploitation and eutrophication-related water quality problems appears 

dependent on a complex mix of factors: river flow, stability of salinity regime, gradients 

in the phytoplankton community due to salinity stress, hydrodynamics and channel 

morphology. Due to this mix of factors, blooms within this reach are neither as regular 

nor predictable as seen for the freshwater river. The near-coastal region outside the 

mouth of the river, presumably due to more favorable light and hydrodynamic conditions,

exhibits more complete utilization of river nutrient loads by algae, and frequently 

supports higher biomass than is seen in the meso-polyhaline river. These off-shore

blooms may at times be imported into the river and contribute to water quality problems. 

In addition to instigating oxygen deficits, there is some suggestion that the supply of 

nitrogen and phosphorus in excess of bioavailable silica concentration may lead to the 

increase in relative abundance of problematic dinoflagellate species in the phytoplankton 

community. 

St. Johns River Water Management District 65
IMPAIRMENT TARGETS FOR IDENTIFYING TMDL AND PLRG NUTRIENT

REDUCTIONS 

Background 

Some measure of the three most commonly identified water quality effects of estuarine

eutrophicationFnuisance levels of algal biomass, reduced dissolved oxygen and reduced 

transparencyFwere recommended in the original Plan document as the response 

variables in establishing nutrient TMDLs and PLRGs for the LSJR. These TMDL and 

PLRG targets were originally established consistent with standards or thresholds set forth 

in Chapter 62-302, F.A.C., the Florida State water quality standards, and Chapter 62-303, 

F.A.C., the TMDL listing criteria for impaired surface waters. In the process of data 

analysis and investigation to describe nutrient enrichment effects and to quantify these 

relationships through water quality modeling, these targets have undergone refinement in 

order to more closely address the most problematic aspects of eutrophication in the LSJR. 

Relevant questions driving the refinement of targets were: 

1) Is the dissolved oxygen State standard sufficiently protective, or conversely, 

unrealistically protective, for biota endemic to the LSJR? 

2) Is the maintenance of transparency, based upon open water changes in 

compensation depth, relevant to SAV health and re-colonization? 

3) Does a mean annual chlorophyll a target sufficiently address acute effects of

extremes in algal biomass characteristic of episodic, intense blooms? 

Because of the weak linkage between open water phytoplankton light attenuation (the 

concept of which is more closely embodied in the transparency standard as stated in 

F.A.C. 62-302) and the more realistic case of epiphytic algal attenuation for littoral 

submerged grasses, it was felt that the transparency criteria could not be sufficiently

justified for protection of SAV in the LSJR. Investigations relating nutrient enrichment 

effects to SAV health, and the interactions between natural factors of light, color, salinity

and substrate are ongoing and can be used to revise the LSJR nutrient TMDL in 

subsequent iterations if warranted. In light of the great amount of research in support of 

St. Johns River Water Management District 66
oxygen criteria, and the recent work accomplished in compiling and refining this research

in EPA:s Ambient Aquatic Life Water Quality Criteria for Dissolved Oxygen (Saltwater):

Cape Cod to Cape Hatteras, (U.S. EPA, 2000) it was felt that the effort necessary to 

modify this guidance approach for the LSJR was not warranted. Therefore, 

methodologies provided in this guidance have been relied upon for establishing algal 

biomass targets for the predominantly marine reach of the river. These methods apply a 

less restrictive criteria for maintenance of aquatic life based on dissolved oxygen than the 

current Florida State Standard, and is arguably more realistic given the natural stressors 

to oxygen level in a southern temperate blackwater river estuary. And finally, as 

experimental evidence suggests that the greatest level of harm from algal blooms occurs 

from extreme bloom events, the chlorophyll a targets for the LSJR were redefined to

emphasize the reduction of high concentration, long duration events. 

LSJR Freshwater Targets: Phytoplankton Community Composition Dynamics, 

Zooplankton Interactions and Algal Toxin Production Potential 

Freshwater LSJR TMDL and PLRG targets on which to base nutrient load reductions 

have been founded primarily on the goal of enhancing plankton ecology. This approach 

was taken because 1) the LSJR is largely a plankton based system, with the majority of 

its autochthonous carbon produced through phytoplankton primary production; 2) 

diversity in plankton assembledges, and the enhancement of energy transfer from 

phytoplankton to zooplankton was assumed to translate to greater abundance and 

diversity in the fish community; and 3) a large data base composed of 5 years of 

phytoplankton and zooplankton monitoring data exists for the LSJR, representing the

most powerful biological evaluation tool available. For the freshwater river, three 

elements of plankton ecology were assessed: 

1) Are there levels of algal biomass at which diversity in the plankton community is 

significantly reduced, i.e., the point of monospecific bloom formation? 

2) What maximum levels of algal biomass, or what phytoplankton community 

composition, is associated with the greatest levels of zooplankton abundance and 

diversity, and, presumably, the greatest upward transfer of planktonic primary 

production to higher trophic levels? 

St. Johns River Water Management District 67
3) What levels of algal biomass minimize the potential for the expansion of 

detrimental algal species or the production of algal toxins? 

Freshwater LSJR Algal Biomass Criteria 

Maintenance of Phytoplankton Diversity 

The maintenance of organism diversity is a fundamental goal of biological restoration. 

Diversity in biological systems promotes stability; conversely, ecosystems with narrow 

species diversity are prone to large perturbations in communities (Wetzel, 2001). The

loss of phytoplankton diversity, and the dominance of cyanobacteria during the spring 

and summer growth seasons is one of the most conspicuous aspects of freshwater blooms

of the LSJR. As total phytoplankton community biomass (expressed as chlorophyll a) 

increases, the fraction of the total community biomass composed of blue-greens 

(determined from biovolume estimates) increases (Figure 38). Blue green relative 

composition is variable and often low for chlorophyll a concentrations to about 40 

mg/m3

. After this point, blue green biomass represents the majority of phytoplankton 

community composition. At chlorophyll a concentration above 60 mg/m3

, blue green 

relative abundance is consistently between 80 to 90 percent. 

Facilitation of Upward Trophic Transfer of Primary Production 

The Chesapeake Bay Water Quality Criteria Guidance Manual (CBP 2002) outlines an 

approach to the development of chlorophyll a criteria for the purpose of enhancing the

upward transfer of phytoplankton carbon to the zooplankton community. The conceptual 

model utilized in the Chesapeake Bay Guidance relating mesozooplankton response to 

increases in algal biomass is depicted in Figure 39. This model is based on a number of 

investigations that have demonstrated the decline of various mesozooplankton species in 

blue-green algal blooms, believed due principally to the presence of noxious compounds

in certain cyanobacteria (Paerl et al., 2001; DeMott and Moxter, 1991; Fulton, 1988). 

At low to moderate phytoplankton densities, zooplankton populations respond favorably 

St. Johns River Water Management District 68
Figure 39. Relationship between blue green relative abundance based on biovolume and 

chlorophyll a for LSJR Freshwater Stations, Nov. 1997 C Oct. 2001. Picolata represented 

by the Watson Island monitoring station in 2000 and 2001 due to high salinity conditions 

at Shands Bridge. Data from Phlips and Cichra, 2002. 

Blue-Green Relative Abundance

0

20

40

60

80

100

0 40 80 120 160

Chlorophyll-a, mg/m3

% Blue-green Composition

Racy Point

Palatka

Picolata

I:\\esdata\lsj\UF=PlanktonID\Data\Zoo-Phyto_Comp.xls

Figure 40. Conceptual model relating mesozooplankton response to increases in algal 

biomass. In average (A) and best (E) water quality conditions, zooplankton increase with 

increasing algal food. Zooplankton increase ceases at some algal biomass (B), at which 

point increases in algae result in lower zooplankton due to the predominance of harmful

or unpalatable species and feeding interference (C1 and C2). Reprinted from the 

Chesapeake Bay Chlorophyll a Criteria Guidance Manual (CBP 2002). 

St. Johns River Water Management District 69
and increase with increase in algal biomass associated with increase in food supply. At 

some point, however, the increase in toxic or otherwise unpalatable taxa in the 

phytoplankton community, and an increase in feeding effort due to the density of 

unfavorable species, leads to a leveling off and perhaps even decline in the desirable 

zooplankton. The point of the departure from the linear increase in zooplankton > 

phytoplankton biomass represents the maximum tolerable algal biomass. 

Plankton monitoring data (Nov. 1996 through Oct. 2001) were examined to determine if

a relationship similar to that described above existed for the freshwater LSJR. The 

zooplankton > algal biomass relationship is shown in Figure 40. Desirable zooplankton 

in these graphs are estimated by summing the organism counts for copepods and 

cladocerns only. Rotifers are excluded, as they are believed to be feeding on small 

detrital particles and bacteria, and are not as important a group of zooplankton in 

supporting the upward transfer of phytoplankton carbon to the fish community. Although 

a good deal of spread exists in this graph in zooplankton abundance at low to moderate 

chlorophyll a concentration, it is possible to discern a pattern that matches the conceptual 

model forwarded by the Chesapeake Bay guidance. This graph suggests that the linear 

increase in zooplankton abundance with increasing chlorophyll a concentration begins to 

decline somewhere between chlorophyll a concentrations of 40 to 60 mg/m3

. The

adverse response of zooplankton numbers to high levels of algal biomass can be seen in 

Figure 41 for the specific case of the severe algal blooms that occurred at Racy Point in 

1999. At this station, zooplankton numbers increase initially as chlorophyll 

concentration increases, but then decline as chlorophyll continues to increase. This

pattern is repeated for the yearTs second bloom, which peaks in late August. 

Algal Toxin Formation Potential 

Paerl and Carmichael (2002) examined levels of the algal toxins microcystin, anatoxin, 

and cylindrospermopsin in nutrient enrichment assays performed on LSJR samples 

collected from October 2000 through August 2001. All toxins were detected during the 

sampling, with microcystin present in every assay. Microcystin was found to be 

St. Johns River Water Management District 70
Figure 41. Relationship between total chlorophyll a and the sum of copepod and 

cladoceran abundance for LSJR freshwater stations at Palatka, Racy Point, Lake George 

and Shands Bridge/Watson Island. Data from Nov. 1996 through Oct. 2001. Green curve 

drawn through visual interpolation. Data from Phlips and Cichra, 2002. 

LSJR Fresh

y = -0.0619x2 + 11.347x - 41.958

R2

 = 0.5348

0

100

200

300

400

500

600

700

800

900

1000

0 20 40 60 80 100 120 140 160

Total Chlorophyll-a, mg/m3

Copepods + Cladocerns, #/ml

Racy Pt.

Palatka

Shands, Watson

L. George

Figure 42. Annual trend in chlorophyll a, total rotifer abundance, and the Copepods + 

Cladoceran abundance for the Racy Point Station in the Freshwater LSJR, 1999. Data 

from Phlips and Cichra, 2002. 

1999

0

20

40

60

80

100

120

140

160

12/31/1998 3/1/1999 4/30/1999 6/29/1999 8/28/1999 10/27/1999 12/26/1999

Chlorophyll a, mg/m3 or Zooplankton, #/ml

Chlorophyll a

Rotifers/100

Copeds.+Clads./10

I:\\esdata\lsj\UF-PlanktonID\VOLUME_ANALYSIS2.xls

St. Johns River Water Management District 71
Figure 43. Microcystin concentrations determined in nutrient addition assays performed 

on freshwater Lower St. Johns River ambient water samples. From Paerl and 

Charmichael, 2002. 

Jul 2000

y = 1.4729x - 3.879

R2

 = 0.5836

Oct 2000

y = 0.0598x + 0.1293

R2

 = 0.5193

Feb 2001

y = 4.9168x - 38.112

R2

 = 0.9053

Apr 2001

y = 3.2444x - 26.315

R2

 = 0.7892

Jul 2001

y = 0.5338x + 106.14

R2

 = 0.0983

Aug 2001

y = 2.2215x + 261.23

R2

 = 0.2186

Oct 2001

y = -0.0272x + 5.1031

R2

 = 0.0124

0

100

200

300

400

500

600

700

800

0 20 40 60 80 100 120 140 160 180

Chlorophyll a, mg/m3

Microcystin, nanog/L

Jul 2000

Oct 2000

Feb-01

Apr-01

Jul-01

Aug-01

Oct-01

 I:\\esdata\lsj\UF-Plankton-ID\algal-tox.xls

positively correlated to chlorophyll a in all assays, and the relationships are shown in 

Figure 42. Generally, microcystin levels remained low for chlorophyll a concentrations

below 40 μg/L. Above this level, microcystin levels were found to be variable, but on 

occasion reached very high levels, near the World Health Organization standard for 

drinking water of 1 μg/L. The LSJR is not a drinking water source, and relevance of this 

standard for the protection of aquatic life has not been quantified. Extremely high 

concentrations of microcystin have, none the less, been measured in the St. Johns and its

tributary mouths. During one bloom response sampling in DoctorTs Lake, microcystin 

concentrations were determined at concentrations ranging from 157 to 211 μg/L (Green 

Water Lab, 2002). The result of these assay experiments suggests that at concentrations 

of chlorophyll a that exceed 40 μg/L, the potential for the appearance of microcystin in 

ambient water increases greatly. 

St. Johns River Water Management District 72
Algal Bloom Duration 

Plankton monitoring data and algal toxin assays indicate that blue green algal blooms of 

the LSJR freshwater reach exhibit detrimental effects when bloom biomass, measured as

chlorophyll a, exceeds 40 mg/m3

. To examine the effect of bloom duration on desirable 

zooplankton, the numbers of copepods and cladocerans in samples collected during 

blooms were compared to the duration of the bloom in excess of 40 mg/m3

 chlorophyll a

(Figure 43). For blooms in excess of 40 mg/m3

 chlorophyll a that exceed 40 days, 

numbers of copepods and cladocerans are noticeably reduced. Between 20 to 45 percent 

of blooms within the freshwater reach exceeded this duration (Figure 20). The maximum 

concentration that is achieved within a bloom is significantly correlated to the bloom 

duration (Figure 44). Based on the linear regressions relating bloom duration to intensity, 

maximum concentrations achieved by a bloom of 40 days range between 50 to 74 mg/m3

chlorophyll a, with a mean of 67.5 mg/m3

. 

Using the Racy Point station, it is possible to synthesize a distribution of chlorophyll a

that hypothetically would meet the conditions for the maintenance of phytoplankton and 

zooplankton diversity. This was done by proportionally scaling the statistical distribution 

Figure 44. Numbers of Copedod and Cladocern zooplankton in samples collected in 

algal blooms of greater than 40 mg/m3

 as a function of the duration of the bloom. 

Zooplankton Abundance vs. Duration of Chlorophyll a > 40 mg/m3

0

100

200

300

400

500

600

700

800

0 20 40 60 80 100 120 140 160 180 200

Duration, Days

Copepods + Cladocerns, #/ml

Racy Point

L. George Outlet

Palatka

St. Johns River Water Management District 73
Figure 45. Bloom maximum chlorophyll a concentration as a function of bloom duration 

for freshwater sampling stations of the LSJR, 1994-2001. 

Bloom Maximum Chlorophyll a x Duration > 40

y = 0.8362x + 40.602

R2 = 0.568

y = 0.4491x + 38.809

R2 = 0.7712

y = 0.5991x + 47.769

R2 = 0.4174

0.0

20.0

40.0

60.0

80.0

100.0

120.0

140.0

160.0

180.0

0.0 20.0 40.0 60.0 80.0 100.0 120.0

Duration > 40 mg/m3, days

Bloom Max Chlorophyll a, mg/m3

Racy Pt.

Federal Pt.

Watson Isl.

of the existing data (shown in Figure 45 by the dark navy blue line; the natural log of 

chlorophyll a is used to normalize the distribution) to form a new, distribution (Figure 45 

light blue line) for which: a) the 1 percentile occurrence was the same as the observed 

data (reflecting the assumption that minimum chlorophyll a values would remain the 

same if nutrient load were reduced); b) the population variance was reduced such that the 

synthetic, new distribution has a 99th percentile occurrence (p = 0.01 for a one tailed test) 

equivalent to a chlorophyll a of 74 mg/m3

. This synthesized distribution has a mean of 

20.1 mg/m3

, a variance of 0.56 mg/m3, and a 10.6 percent occurrence rate for chlorophyll 

a concentrations greater than 40 mg/m3

. The synthesized distribution thus suggests 

fairly good agreement between a not to be exceeded level of 10% for blooms in excess of 

40 mg/m3, and the mean concentration of 20 mg/m3 of the recently promulgated TMDL 

listing rule of F.A.C. 62-303. 

St. Johns River Water Management District 74
Marine LSJR Dissolved Oxygen Criteria 

Dissolved Oxygen Effects 

As demonstrated in the previous section outlining eutrophication effects, low dissolved 

oxygen excursions (persistent episodes below the State criteria of 5 mg/L) occur in both 

the freshwater and oligo/mesohaline reaches of the LSJR. These episodes occur 

coincident with high summertime temperatures, and appear to be associated with the 

decline or crash of significant algal blooms. The improvement of the dissolved oxygen 

regime for the river and estuary was one of the originally stated objectives of the TMDL 

and PLRG plan for the river, and the State standard of 5 mg/L (instantaneous for

freshwater reaches, and as a daily average for predominantly marine reaches) was 

identified as the target on which to base nutrient reduction scenario modeling. Even at 

the time of the proposition of this target, however, considerable uncertainty existed

regarding its appropriateness and achievability. Low dissolved oxygen episodes have 

long been known to occur in southeast U.S. estuaries (Schroeder and Wiseman, 1988), 

and naturally low dissolved oxygen concentrations are a commonly accepted feature of 

blackwater river systems. For these reasons, effort has been directed toward refining an 

oxygen regime that is based upon the levels necessary for the protection of native 

estuarine fish and invertebrate species. 

As an alternative to the fixed standard of 5 mg/L, the procedure described in the recently 

published U.S. Environmental Protection Agency Guidance, Ambient Aquatic Life Water

Quality Criteria for Dissolved Oxygen (Saltwater): Cape Cod to Cape Hattaras, (U.S. 

EPA, 2000) has been used to define the dissolved oxygen target on which reductions of 

algal biomass, achieved through nutrient load reduction, can be based. The Guidance is

built upon the established tolerances of fish and invertebrates present in the estuarine 

environment to low oxygen episodes. In its approach, the Guidance establishes an 

absolute minimum oxygen level for the protection of most estuarine species against low

concentrations that result in acute organism mortality, and establishes above this level a 

sub-lethal range that results in reductions in growth and recruitment, and with this, 

St. Johns River Water Management District 75
Figure 46. Observed and synthesized distributions for total chlorophyll a at Racy Point 

in the freshwater LSJR. Observed data based on sampling from 1994 through 2001; n = 

191. 

Racy Pt - RKm 100 

0

10

20

30

40

50

60

70

80

90

100

1.2 1.4 1.6 1.8 2 2.2 2.4 2.6 2.8 3 3.2 3.4 3.6 3.8 4 4.2 4.4 4.6 4.8 5 5.2

Ln (Chlorophyll a, mg/m3)

Percent Rank

presumably fish health and survival probability. Fish community effects within this sublethal range are based upon the intensity and duration of hypoxic events. The Guidance

also offers approaches for assessing effects of two common types of low dissolved 

oxygen common to eutrophic estuaries: persistent, low dissolved oxygen associated with 

late season algal bloom decline; and diurnal patterns of low oxygen associated with high 

algal standing stock photosynthesis and respiration cycles or tidal transport of low

oxygen water masses. In the LSJR, the most common and severe low oxygen episodes 

within the oligo/mesohaline reach are persistent events associated with late season algal 

community decline, and the Guidance procedure for assessing these types of events has 

been used to define oxygen targets. 

Organism Acute Oxygen Levels 

The data set used in the Guidance to develop criteria minimum concentration (CMC) was

assimilated from previous studies that examined species or genus-specific survival under 

continuous low dissolved oxygen exposures. These studies covered 12 invertebrate and 

St. Johns River Water Management District 76
11 fish estuarine species, mostly at juvenile life stages. Of these 23 species, 12 are 

known to inhabit estuarine waters of northeast Florida, based upon sampling performed 

by The Florida Marine Research Institute (FMRI, 2002), Coasta Shelf Associates (CSA 

Inc., 1993) and Whitney Marine Lab (Table 4). From the FMRI non-game fisheries 

monitoring data (FMRI, 2002) a trend is evident between the numbers of individuals of a

given species present, and the low oxygen LC50 value of the Guidance, in that as an 

individual species low dissolved oxygen tolerance decreases, its abundance declines in 

the northeast Florida sampling region. A number of factors could account for this,

including species natural ranges, sampling methodology, migration patterns or 

competitive interactions, though the possibility that these species are excluded due to

prevailing low dissolved oxygen, either as a natural occurrence or through accelerated 

eutrophication, should be considered as a potential contributing factor. 

Following the procedure established in the development of toxics criteria, the Guidance

adjusts the CMC upward to estimate an LC5 concentration, using the mean LC5/LC50 

ratio for all studies, applied to the most sensitive species mean acute value (SMAV). In 

the studies compiled in the Guidance, pipe fish (Syngnathus fuscus), exhibited the highest 

SMAC, at an LC50 concentration of 1.63 mg/L. Pipe fish has been reported in northeast 

Florida region in all sampling studies, albeit at low numbers. Because of the number of 

species present in North Florida in common with those listed in the Guidance, including

the presence of the most sensitive species (pipe fish), the Guidance CMC value is viewed 

as protective for the LSJR. The Guidance CMC, determined as the product of the mean

LC5/LC50 ratio (1.38) and the most sensitive species LC50 (1.63 mg/L), is 2.3 mg/L. 

Growth Effects 

To develop a measure of sub-acute effects due to low dissolved oxygen, the Guidance

relied upon previous studies that examined reductions in fish growth, usually during 

larval or juvenile life stages, due to low dissolved oxygen concentration. Growth is

usually more sensitive than survival to low dissolved concentrations, though the 

St. Johns River Water Management District 77
Table 4.Saltwater Animals Upon Which Low Dissolved Oxygen Tolerances of the EPA Saltwater Dissolved Oxygen Criteria

Are Based That Have Been Reported in Northeast Florida. Species occurrence data from FMRI (2002), Coastal

Shelf Associates, and from the Whitney Laboratory web site (http://www.whitney.ufl.edu/species/availabl.htm). 

Species Common Name FMRI Whitney Lab CSA, Inc.

Palaemonetes vulgaris marsh grass shrimp freq

Palaemonetes pugio daggerblade grass shrimp freq

Callinectes sapidus blue crab 861 freq

Eurypanopeus depressus flat mud crab x

Rithropanopeus harrisii Harris mud crab x

Crassostrea virginica eastern oyster freq

Leiostomus xanthurus spot 4333 freq freq

Prionotus tribulus bighead searobin genus

Brevoortia tyrannus Atlantic menhaden 788 freq

Paralichthys dentatus summer flounder 9 rare genus

Syngnathus fuscus pipe fish 1 rare genus

Morone saxatilis striped bass freq

Guidance notes several exceptions in which studies report greater rates of mortality than 

growth reduction. In general, invertebrates exhibit low acute dissolved oxygen 

concentrations, but a large range in growth reduction. Fish, on the other hand, exhibit 

higher acute concentrations but a relatively narrow range in growth reduction, and it is 

not unusual for fish species to exhibit considerable overlap in oxygen levels that cause 

mortality and growth reduction. Based upon a smaller number of studies that reported 

similar reductions in reproductive success at low dissolved oxygen levels, the Guidance 

concluded that oxygen levels that are protective of growth effects would also likely be 

protective of reproductive success. 

Of the 11 species for which growth effects data were found, 5 have been reported in 

FMRI, CSA, Inc. or Whitney Lab sampling, or are otherwise know to occur here at the 

species level: summer flounder (Paralichthys dentatus), sheepshead minnow 

(Cyprinodon variegates), striped bass (Morone saxatilis), marsh grass shrimp 

(Palaemonetes vulgaris), northern quahog (Mercenaria mercenaria). Silverside 

(Menidia) and spider crab (Libinia) are also reported to occur here at the genus level. 

The reported no observed effects concentrations (NOEC; concentrations above which 

St. Johns River Water Management District 78
reduction in growth was not observed in studies) for these species range from 2.5 to 7.23 

mg/L, with a species mean of 4.63 mg/L. Based upon these ranges and the species mean 

value, it appears that the final chronic value (FCV) at which low dissolved oxygen is not 

expected to effect growth of 4.8 mg/L as suggested by the Guidance is appropriate for 

northeast Florida. 

Larval Recruitment 

To estimate the effects of hypoxic conditions at concentrations between 2.3 and 4.8 

mg/L, the Guidance applies a larval recruitment model to estimate the number of 

individuals that are JrecruitedK from early life stages to juvenile stage. This model is

based upon larval development time, larval season, attrition rate and patterns of vertical

distribution. The larval recruitment model can be adapted with regionally specific data if 

available. No attempt has been made to parameterize the larval recruitment model for the 

LSJR, and the model formulation as provided in the Guidance has been used for

evaluating the organism effects due to low dissolved oxygen. Nine genra had sufficient 

data to parameterize the model as developed in the Guidance. Six of these, Menidia,

Scianops, Palaemonetes, Eurypanopeus, Libinia and Morone, are known to be present in 

northeast Florida. 

Application of the Criteria 

The maximum acute value, growth effects threshold and larval recruitment model are 

combined into one relationship relating the intensity and duration of a given continuous, 

low dissolved oxygen event. This approach is graphically depicted in Figure 46. Above 

4.8 mg/L, estuarine organisms are assumed to suffer no chronic effect from hypoxia 

(defined as dissolved oxygen below saturation concentration; for example, oxygen 

saturation concentration at 30 o

C and 15 ppt chlorinity = 6.5 mg/L). Oxygen levels below

2.3 mg/L are expected to have acute lethal effects to at least some organisms. Between 

these two values, the degree of mortality in the population is proportional to the duration

of exposure. A given interval of low dissolved oxygen is considered to be a JdoseK of 

St. Johns River Water Management District 79
potentially low dissolved oxygen, and is expressed as the fraction of the total duration of

the interval at that concentration needed to cause mortality in at least 5% of the most 

sensitive species of the fish community. For example, the impairment index calculated 

duration of exposure to dissolved oxygen at 3 mg/L is 5.57 days. A one-day duration of 

3 mg/L dissolved oxygen is considered to be 1/5.57 or 18% of a lethal dose. Individual 

doses of continuous exposure that sum up to greater than 1 are considered to represent a 

lethal dose. 

Following the approach, 3 out of the 6 years of data collected at the Dames Point station 

exhibited at least one, long excursion of continuous low oxygen that exceeded the 

impairment threshold. Durations of these events ranged from 4 to 7 weeks. Calculated 

impairment scores for Dames Point were 1.74, 3.57, and 1.14 for 1997, 1999 and 2001. 

In 1999, a large fish kill of many thousands of adult shad and menhaden occurred in this 

Figure 47. Graphical representation of the long term chronic exposure threshold 

relationship defined in the Ambient Aquatic Life Water Quality Criteria For Dissolved

Oxygen (Saltwater): Cape Cod to Cape Hatteras (2000). 

Dissolved Oxygen Supression - Duration: Continuous 

Events

0

1

2

3

4

5

6

0 200 400 600 800 1000 1200

Hours

Minimum Tolerable D.O.

Chronic Protection Value = 4.8 mg/L

Survival Level = 2.3 mg/L

Assessment Range

I:\\esdata\lsj\WESWQMod\Calibration

Data\Marine CtoCHLA.xls

St. Johns River Water Management District 80
reach of the river, associated with this low D.O. event. No low D.O. events were 

measured at the Acosta Bridge station between 1996 and 2001 that qualify for chronic 

impairment under the EPA guidance approach, with the greatest score being 0.73, 

recorded in 1998. 

Additional Considerations 

The methodology descried in the EPA estuarine dissolved oxygen guidance addresses 

only acute and chronic (growth) direct effects from low dissolved oxygen. Because of 

predator-prey interactions, the timing of reproductive activities, additional stressor effects 

under conditions of nutrient enrichment and eutrophication, direct effects may be

mitigated or enhanced. Breitburg (2002), in her review of hypoxia effects, addresses 

many of the permutations of trophic alterations that may potentially occur as a result of 

low oxygen-induced mortality in various segments of the coastal fish population. An 

important aspect of low dissolved events in the LSJR is that they tend to be vertically

uniform and extending for significant length. Such slugs of low dissolved oxygen water 

offer little refuge for motile fish, and can effectively trap large numbers of animals when 

low oxygen-favoring hydrodynamic factors and feeding or migratory patterns intersect. 

While the approach used is expected to be appropriate for other regions outside the 

Virginian Province estuaries, the Guidance does note that animals may have adapted to 

lower oxygen levels in regions of higher temperatures or with naturally high demands for 

dissolved oxygen. In particular, it may be appropriate at some point to develop 

regionally specific data for revising the larval recruitment model on which cumulative, 

sub-lethal effects are based. At the present time, however, in lieu of specific recruitment 

studies for northeast Florida, the Guidance approach represents a means to judge the

impact of low dissolved oxygen events, that is supported in a number of independent 

studies on species that are present in large numbers in the lower St. Johns River, and is 

less arbitrary than the application of a strict 5 mg/L standard. 

St. Johns River Water Management District 81
Dinoflagellate Bloom Potential 

Nutrient and organic matter enrichment leading to the stimulation of growth of marine 

dinoflagellate algal species represents a potentially detrimental effect attributable to

estuarine eutrophication. Several toxic dinoflagellate species have been identified in 

regular plankton monitoring, including Karenia brevis (red tide) and Prorocentrum 

minimum, and dinoflagellate infections have been postulated as a possible factor in 

ulcerative disease syndrome that plagued the LSJR during much of the early 1990Es. A 

monitoring program conducted in the mid-1990Es, with the objective of determining the 

presence of PfiesteriaIlike species, discovered a previously unidentified dinoflagellate, 

subsequently named Cryptoperidineopsis brodii, present in LSJR mesohaline reach

sediments. 

The tendency for dinoflagellate populations to increase in relative abundance under

conditions of increasing potential diatom silica limitation leads to the possibility that high 

levels of nitrogen and phosphorus enrichment, in excess of that balanced by bioavailable 

silica, may contribute to dinoflagellate blooms. In a recent review on the effects of the 

changes in nutrient ratios on estuarine plankton food webs, Turner (2002) cites numerous 

studies that demonstrate the cause for concern that N and P increases may increase the 

potential for harmful dinoflagellate blooms. Dinoflagellate life cycles and survival 

strategies are extremely complex, however, and occurrence of high populations in the 

LSJR is poorly correlated with nutrient concentration or diatom biomass. For this reason, 

the limitation of dinoflagellate blooms exists as a qualitative target in LSJR TMDL

development. The reduction of dinoflagellate bloom potential as a water quality

restoration goal is not without precedent. In recent work investigating the relationship

between nutrient enrichment effects on nuisance algal growth in the Indian River Lagoon, 

the occurrence of potentially toxic dinoflagellate blooms is identified as a significant 

water quality impairment (Phlips et al. (2003)). And in recently proposed algal biomass

criteria for Chesapeake Bay (CBP, 2000), the increase in the incidence of the potentially 

St. Johns River Water Management District 82
toxic dinoflagellate Prorocentrum minimum at detrimental biomass levels is used to

support the maintenance of chlorophyll a levels below 25 mg/m3. 

St. Johns River Water Management District 83
RECOMMENDATIONS

Water Quality Model Enhancements 

Based upon the examination of existing water quality data and the results of 

investigations on algal community composition and nutrient utilization patterns, the 

following findings should be integrated into the modeling of eutrophication of the LSJR 

for the determination of nutrient pollution assimilative capacity (TMDLs) and nutrient 

pollution reductions (PLRGs). 

1) Blue green nitrogen fixation provides a significant contribution to the riverOs total 

nitrogen budget, and must be included in the water quality modeling for the 

TMDL and PLRG. Nitrogen fixation rates appear to be variable, based upon the 

adequacy of external phosphorus availability. Anabaena appears to be the most

prominent N-fixer when external phosphorus supply is high, and 

Cylindrospermopsis the most abundant when P supply is low. 

Cylindrospermopsis, based upon assay work under increasing levels of salinity 

(Paerl et al, 2002), showed the lowest levels of salinity tolerance, with effects

evident at salinity below 2 ppt. Thus, model algorithms should begin to reduce 

blue green N-fixation at these low salinities. In addition, more field studies 

should be performed to determine the parameters of growth, N-fixation, nutrient 

limitation, toxicity and potential food web effects of these two important bloomforming species. 

2) Comparison of model stoichiometry to measured data demonstrates good 

agreement to standard Redfield ratios. A curvilinear relationship between

particulate P and algal C tends to support the choice of Droop kinetics (Droop, 

1973) in the LSJR application of CE-QUAL-ICM for modeling the uptake and 

sequestration of phosphorus. Comparison of chlorophyll a to particulate organic 

carbon supports the choice of a carbon:chlorophyll a ratio of 50:1. A minimum 

phosphorus cell quota of between 0.02 to 0.01 P:C is suggested by monitoring 

St. Johns River Water Management District 84
data collected, based upon samples with high algal carbon and low PO4

concentration. 

3) Zooplankton abundance clearly exhibits declines associated with high 

concentrations of blue green algal biomass. To mimic this effect in water quality 

modeling, algal predation rates should be reduced at high levels of blue green 

algal carbon. 

4) Extended periods of phosphorus limitation in freshwater blue green algal blooms

appears to result in precipitous bloom crashes. The CE-QUAL-ICM model has 

no mechanism to trigger such a bloom collapse. Because these crashes seem to be 

associated with some extended period of very low external orthophosphate 

concentration, the recommendation for modeling is to trigger rapid senescence in

freshwater blue green blooms when phosphorus cell quota reaches some very low

level. 

5) The transition from the oligohaline, low-salinity tolerant, diatom, dinoflagellate

and blue green-dominated community to the marine diatom community is 

believed to be an important aspect of mesohaline reach low dissolved oxygen 

levels. In order to capture this in the water quality model, the 3 available algal 

groups should be re-aligned to represent the following: a primarily freshwater 

community dominated by blue greens and represented by blue green settling, 

uptake and growth coefficients; a mildly salt tolerant community, with senescence 

triggered by salinities in the 18 R 25 ppt range, and dominated by freshwater 

diatoms; and a marine community, with a programmed freshwater intolerance, 

dominated by marine diatoms. 

6) Original intentions in modeling were to use the 1997 as a calibration year. 

However, due to the large RGC Mine spill that left much of the freshwater reach

opaque during the peak of the spring algal bloom season, it is recommended to 

shift calibration to the years 1998 and 1999. These two years also offer largely 

contrasting settings of flow and nutrient limitation, which should improve

calibration range. 

St. Johns River Water Management District 85
Water Quality Targets to be Attained Through Nutrient Reductions 

Within the freshwater reach of the LSJR, regular, intense spring and summer algal 

blooms were found to reduce the numbers of beneficial zooplankton, lead to intense, 

rapid collapses in dissolved oxygen, and present potential harm through the formation of 

cyanotoxins. To mitigate these impacts, blooms in excess of chlorophyll a concentration 

of 40 mg/m3

 should not be present for greater than 10% of the time. As a secondary 

threshold, maximum algal biomass should not exceed 70 mg/m3

 at any time. 

The attainment of a more favorable dissolved oxygen regime is the goal of the nutrient 

reductions in the oligohaline and mesohaline reaches of the LSJR. Biodegrading organic 

matter in this reach, which appears to be dominated by algal organic matter, should not 

exceed that which would trigger a continuous, persistent chronic level of low oxygen, 

based on the approach outlined in the U.S. EPA guidance, Ambient Aquatic Life Water

Quality Criteria for Dissolved Oxygen (Saltwater): Cape Cod to Cape Hattaras (U.S. 

EPA, 2000). A number of potentially overlapping factors, such as the intensity off-shore, 

near-coastal blooms imported to the river through reverse tides, upstream algal detrital 

load, and the location of the polyhaline transition all appear to play a role in the severity

of low oxygen events. Because of these intricacies, it is suggested that modeling of 

nutrient load reductions not be directed to the achievement of an algal biomass level, but 

rather to the achievement of the persistent, chronic low dissolved oxygen impairment 

index described in the EPA guidance. 

St. Johns River Water Management District 86
LITERATURE CITED 

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on coastal fishes and fisheries. Estuaries 25:4b (767-781). 

CBP, 2002. Chesapeake Bay Water Quality Criteria: Chapter 5 Chlorophyll a Criteria.

Chesapeake Bay Program Website. 

http://www.chesapeakebay.net/pubs/waterqualitycriteria/12022002/Chapter5.pdf

Cerco, C.F. and T. Cole. Three dimensional Eutrophication Model of Chesapeake Bay. 

J. of Environmental Eng. 119:1006-1025. 

Cerco, C.F., M.R. Noel and D.H. Tillman. 2003. A practical application of Droop 

kinetics. Manuscript in review. 

Chapra, S.C. 1997. Surface Water Quality Modeling. McGraw Hill, New York, NY. 

CSA, Inc. 1993. Fish Assemblages Inhabiting an Oligohaline Segment of the Lower St. 

Johns River, Florida. St. Johns River Water Management District Special Publication 

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DeMott, W.R. and F. Moxter. 1991. Foraging on cyanobacteria by copepods: Responses 

to chemical defenses and resource abundance. Ecology 72(5): 1820-1834. 

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Freshwater Biol. 20: 263-271. 

Green Water Labs. 2002. Bloom response reports to the St. Johns River Water

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Huber, W.C., P.L. Brezonik, J.P. Heaney, R.E. Dickinson, S.D. Preston, D.S. Dweornik 

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the Effects of Nutrient Pollution. National Academy Press, Washington D.C. 

St. Johns River Water Management District 87
Paerl, H.W., M.F. Piehler, W.W. Carmichael, J. Dyble, P.H. Moisander, J. Leonard and 

A.Waggener. 2002. Phytoplankton and zooplankton in the St. JohnDs River System:

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River Water Management District under Contract No. SD154RA. 

Paerl. H.W., R.S. Fulton, III, Miosander, P.H, and J. Dyble. 2001. Harmful Freshwater 

Algal Blooms, with and Emphasis on Cyanobacteria. The Scientific World 1: 76-113. 

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Community of the Lower St. Johns River. Final Report to the St. Johns River Water 

Management District, Contract No. 97W165. 

Phlips , E.J., S. Badylak and T. Grosskopf. 2003. Nutrient limitation of phytoplankton 

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Management District. 45 pp. 

Pyatt, E.E. 1964. On determining the pollutant distribution in tidal estuaries. U.S. 

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Water Resources Department Technical Memorandum. 

Turner, R.E. 2002. Element ratios and aquatic food webs. Estuaries 25(4b): 694 e 703. 

U.S. EPA. 1985. Rates, Constants, and Kinetics Formulations in Surface Water Quality 

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U.S. EPA. 2000. Ambient Aquatic Life Water Quality Criteria for Dissolved Oxygen 

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Water, Washington D.C. EPA-822-R-00-012. 49 pp. 

St. Johns River Water Management District 88
Verity, P.G., J.A. Yoder, S.S. Bishop, J.R. Nelson, D.B. Craven, J.O. Blanton, C.Y. 

Robertson and C.R. Tronzo. 1992. Composition, productivity and nutrient chemistry of a

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