Seagrasses have occupied shallow marine environments for approximately the
past 100 million years (Duarte 2001). In that time, the 60 or so worldwide
seagrass species have persisted in the face of continual environmental
change, including global climate shifts and changing sea levels. Much more
recently-perhaps the last 100 years or so-seagrass ecosystems throughout
much of the world have been subjected to new survival challenges posed by
manmade alterations to the environment. Many of these changes are
occurring very rapidly, and complex biological systems such as seagrass
habitats are not equipped to adapt to rapid environmental change.
Light availability is essential for seagrass beds to thrive and grow. The
seagrass species that inhabit the IRL all have relatively high light
requirements and the distribution of seagrass habitats in the lagoon is
restricted to those shallow areas where water clarity is sufficient to
allow adequate light penetration. Water quality conditions that impede the
penetration of sunlight to the benthic environment threaten seagrass
A number of human activities within the IRL watershed have impacted the
seagrass habitats of the lagoon. The most significant of these are
salinity fluctuation due to altered hydrology and stormwater runoff,
dredging and increased sediment loading, and increased nutrient and
chemical pollutant loading to the lagoon. Biotoxin accumulation is another
emerging issue impacting the health of seagrass community components. Each
of these issues, their effect on IRL seagrass communities, and current
efforts directed at finding solutions are discussed below.
Hydrologic Alterations and Excess Freshwater
For most of the IRL seagrasses, a salinity of 20 ppt appears to be optimal
for growth (wigeongrass, Ruppia maritima, is the exception, growing best
under less saline conditions). The spring-summer seagrass growing season
coincides with Florida's wet season, however, and local salinities often
drop below this optimum during this period. Seagrasses can survive
exposure to lower salinities but growth is impacted. If low-salinity
conditions persist for an extended period, however, seagrass bed health
will suffer and dieback is likely (Hanisak 2002).
A defining feature of the IRL is that it is an estuary, occupying the
narrow boundary between land and sea and connected to the Atlantic
Ocean by five narrow inlets. The salinity regimes within specific
segments of the 250 km-long system are largely determined by proximity
both to ocean inlets and to various surface freshwater inputs like
streams, rivers, canals, and ditches. Limited water exchange with the
ocean through inlets spaced unevenly down the length of the system
gives rise to an estuary that is very sensitive to the volume and
timing of freshwater discharged to it from the surrounding watershed
(the area of land from which water drains to a receiving water body).
The historic IRL watershed was around 231,480 ha (572,00 acres). Since
around 1916, however, the creation of drainage canals to increase
agriculture production and for flood control has artificially enlarged the
IRL watershed to the west, to include land that did not naturally drain
into the lagoon. Fresh water that historically drained into the St. Johns
River or Lake Okeechobee, for example, now flows to the lagoon instead.
The area of the IRL watershed has been artificially increased to more than
566,000 ha (1.4 million acres). This means that the lagoon now receives
freshwater discharge from two-and-a-half times more land than it did a
century or so ago. The long-term result has been a dramatic decline in
lagoon water quality, and in seagrass health. Declines in IRL seagrass
coverage have been documented since the 1950s, with 100% loss recorded in
some areas (Haddad 1985). The declines correlate with increased turbidity
and general water quality decline (Morris and Tomasko, 1993). For a more
detailed look at seagrass coverages trends over time in the lagoon, click
The health of animals comprising the seagrass ecosystem is also
affected by fluctuating salinity. For example, the planktonic eggs of
spotted seatrout and other fish fail to maintain buoyancy under
low-salinity conditions. The distribution of these eggs within the
water column, as well as their health and survival, is therefore likely
to be influenced by localized salinity conditions (SJRWM 2007). In
addition, oysters, clams and other animals, including the larval forms
of many lagoon organisms, are sensitive to fluctuations in salinity as
well. Hard clams (Mercenaria mercenaria) can briefly tolerate
salinities as low as 15 ppt, and eastern oysters (Crassostrea
virginica) survive at salinities as low as 2 ppt. However,
seasonal low salinity conditions-particularly those caused by wet
season stormwater discharges to the lagoon through the drainage canal
network-can temporarily reduce local salinities such that the health
and survivorship of these and other organisms are compromised. A
three-week long controlled freshwater discharge of approximately 70
cubic meters (2,500 cubic feet) per second from Lake Okeechobee through
canal C-44 into the St. Lucie Estuary in the southern end of the IRL
system in the early 1980s resulted in a localized drop in salinity to a
minimum of 0.5 ppt. This discharge event resulted in significant
change in the benthic and fish communities, including loss of species
both through mortality and avoidance and the establishment of some
freshwater species (Haunert and Startzman 1985, Strom and Thompson
Nonpoint source (i.e., no single identifiable source) pollution,
generated over a wide area, contributes significantly to the pollutant
load discharged into the IRL. Stormwater discharges are one type of
nonpoint source pollution. The IRL watershed typically receives around
127 cm (50 inches) of rain a year, with most of that coming in the
spring-summer wet season. While much of this stormwater runoff is
destined to flow to the estuary by definition, how it gets there is now
very different than it was historically. Prior to the human
development or the IRL watershed area occurrong during the last
century, most rainfall within the IRL watershed fell onto upland
habitats where it would percolate through permeable soils and then
slowly travel to the lagoon. On the way, much of the precipitation
would be taken up by vegetation and the remainder would be naturally
scrubbed of contaminants as it made its way to the estuary. By the
time it entered the lagoon, this water would have been relatively
clean. Now, however, impermeable surfaces like roads, parking
lots, and rooftops cover much of the area where this natural
cleaning process once occurred. Large volumes of stormwater runoff
today rapidly flow into creeks, streams, canals, and ditches, and
then to the lagoon. Sediments, decomposed organic matter,
nutrients, heavy metals, viruses and bacteria, and other pollutants
are swept up in the runoff and carried to the lagoon.
All of the excess fresh water entering the lagoon carries with it a
nutrient and pollutant load that further impacts the health of the IIRL
ecosystems. Excess nutrients promote the growth of water column
phytoplankton and seagrass epiphytes which preempt light before it reaches
the seagrass. Dense phytoplankton blooms also reduce light penetration by
elevating water column color and turbidity (Kenworthy and Haunert 1991,
Morris and Tomasko 1993).
Increasing nutrient concentrations also correlate with decreasing dissolved
oxygen (Dodds and Welch, 2000). Biotic breakdown of the increased biomass
generated by algal primary producers increases oxygen demand. The primary
producers themselves also reduce oxygen levels during nighttime respiration
in the absence of photosynthesis.
Examination of a single large canal-the C-25 Canal in the south IRL
region-hints at the magnitude of the nutrient loads entering the IRL. This
canal system drains an area of approximately 15,380 ha (38,000 acres) in
Indian River and St. Lucie Counties and discharges into the lagoon through
a control structure on Taylor Creek. The canal releases an average of
nearly 212 million cubic meters (56.5 billion gallons) per year of
freshwater. This volume of water carries with it more than 280 tons of
nitrogen and nearly 40 tons of phosphorus (FDEP 2003).
Residential septic systems are another source of nutrient loading to the
lagoon. Although each septic system discharges only a small amount of
nutrients to the environment, the cumulative impact of all such discharges
is substantial. Septic system discharge may also contribute to elevated
levels of bacterial contamination.
Turbidity, Sediments, and Muck
Sediments entering the lagoon can affect water column turbidity and light
penetration, potentially diminishing seagrass productivity. Most sediments
that naturally occur in the lagoon are relatively large in the silt, sand,
and shell fragment size classes. The are generally too heavy to become
resuspended in the water column and therefore have little effect on water
clarity. However, about 10% of the lagoon bottom is covered with a loose,
fine-grain, organic-rich black mud commonly referred to as 'muck.'
Typically found in deeper areas such as dredged channels and the
Intracoastal Waterway (ICW), these deposits settle onto bottom habitats,
potentially smothering organisms or blocking light penetration. Muck is
also found at or near the mouths of most of the major freshwater
tributaries of the lagoon, with the tributary mouths acting as traps
capturing these sediments before they enter the lagoon proper.
Muck harms fish, shellfish, and the seagrasses they inhabit. It is easily
stirred up and resuspended by boats as well as storms, leading to elevated
turbidity and decreased light penetration. Muck deposits frequently also
havehigh levels of heavy metals such as copper, lead, and zinc. Heavy
metals can be toxic to marine life, with effects ranging from illness to
reproductive failure and mortality.
News headlines are increasingly occupied by stories relating outbreaks of
human illness to the consumption of tainted seafood. The bioaccumulation
of environmental toxins in the tissues of lagoon fish and shellfish is
certainly cause for concern from a human health standpoint. From the
standpoint of the environmental health of the IRL, biotoxins are also of
Harmful algal blooms (HABs) are the most common source of deleterious
environmental biotoxins in Florida's marine environments. Harmful
blooms of the dinoflagellate Karenia brevis, and to a lesser
extent other dinoflagellates, are responsible for Florida's red tides.
The brevitoxins produced by red tide are capable of killing fish,
birds, and other marine animals, and can also cause severe human health
problems (FWRI undated). Ciguatera toxin is another well-known marine
toxin, although it is less prevalent in Florida than other biotoxins.
Ciguatera toxin is produced by cyanobacteria (blue-green algae) and
increasingly accumulates in the tissues of successive consumers up the
food chain. Ciguatera toxin causes severe gastrointestinal and
neurological illness when ingested by humans.
Other Biotoxins: Tetrodotoxin is the toxin responsible for the puffer
fish toxicity that sometimes strikes consumers of Japanese fugu. But
in 2002, a different toxin called saxitoxin was revealed to be the
culprit in 19 cases of human poisoning involving puffer fish from the
IRL (SJRWMD 2007). Unlike tetradoxin, saxitoxin is not concentrated
within certain organs of the fish, and it can't be removed from the
fish or detoxified by cooking or freezing (Brevard County Health
Department undated). Saxitoxin was also implicated as the toxin
produced in a 1996 IRL bloom of the dinoflagellate Gymnodinium
pulchellum that resulted in a series of fish and invertebrate
kills. Catfish, mullet, snook, redfish, blue crabs, and penaeid shrimp
were among the animals affected (Steidinger et al. 1998).
Disease-causing organisms: Also affecting the health of animals in the
lagoon is a number of infectious diseases that are not yet entirely
understood. Among them are a viral fibropapilloma that causes
unsightly and life-threatening tumors on green (and, to a lesser
extent, loggerhead) sea turtles inhabiting the IRL (Hirama and Ehrhart.
2007). A fungal pathogen called lobomycosis infects a significant
percentage of the IRL bottlenose dolphin population (Reif et al.
2006). Lobomycosis is a chronic cutaneous and subcutaneous
infection resulting in ulcerative skin lesions that can cover much
of the infected animal's body. The condition is contractible by
humans, adding to the urgency of better understanding the IRL
Working Towards Solutions
Critical as water clarity is to seagrass health, restoring water clarity is
a central goal of initiatives designed to improve IRL seagrass health. A
key element of current efforts to protect and restore the lagoon's
seagrasses is the improved management of freshwater discharges and their
associated pollutant loadings. Multiple entities are engaged in the design
and implementation of projects aimed at reducing and better managing the
quantity and quality of freshwater entering the estuary. The scale of
these projects ranges from modest to very large, and from local to
Artificial salinity fluctuations, elevated nutrient levels, and excessive
muck deposits are all the result of an extensive man-made drainage system
that delivers large quantities of fresh water and associated pollutants to
the lagoon. Abatement actions aimed at correcting these issues share the
common goal of reducing the volume of fresh water discharged to the lagoon.
The largest IRL hydrological restoration project contemplated to date is
the long-delayed, recently commenced Indian River Lagoon-South project, a
critical component of the $8 billion, 30-year Comprehensive Everglades
Restoration Plan (CERP). The goal of the CERP is to restore, protect and
preserve the water resources of central and southern Florida, including the
The Indian River Lagoon-South project is a large-scale freshwater
rediversion. Its intent is to improve water quality and mediate salinity
fluctuations within the St. Lucie Estuary (SLE) and the southern Indian
River Lagoon by reducing total and peak freshwater discharges and by
reducing nutrient, pesticide, and pollutant loads. The Indian River
Lagoon-South project plan: 1) includes
170,000 acre-feet of water storage (reservoirs C-44, C-23 and 24 North and
South, and C-25) and storm water treatment areas (C-44, C-23, C-24 and
C-25); 2) provides water storage on 37,000 ha (92,000 acres) of natural
storage areas (Allapattah, Palmar, and Cypress Creek); and 3) removes more
than 8 million cubic meters of muck from the St. Lucie River and Estuary.
Stormwater mitigation programs exist at several levels. At the local
level, municipal governments in the lagoon region have stormwater utilities
charged with developing and implementing plans to address flooding,
stormwater systems operation, and water quality. The local governments are
also subject to the National Pollutant Discharge Elimination System (NPDES)
stormwater permiting program authorized by the Clean Water Act to regulate
stormwater discharge to surface waters.
One of the current stormwater management initiatives being implemented along the entire lagoon is the installation of large sediment traps, sometimes
called "baffle boxes," designed to capture suspended sediments and
particulate debris and remove them before they reach the lagoon via the
drainage network (IRLNEP 2006).
The Water Management Districts operating within the IRL watershed have
undertaken development of specific Pollutant Load Reduction Goals (PLRGs)
for the lagoon, while the Florida Department of Environmental Protection
(FDEP) is charged with establishing Total Maximum Daily Load (TMDL)
requirements for pollutants. The water quality standards established by
these agencies will be based on the ecological needs for a healthy IRL
seagrass community. Once set, programs and projects will be developed and
implemented to meet the new standards (SJRWMD 2007).
Nutrient Loading Reduction
In 1990, a big step was taken toward reducing point source nutrient loading
when the state legislature passed the Indian River Lagoon Act. This act
mandated that domestic wastewater treatment plants cease discharging their
effluents to the lagoon by July 1996. Elimination of this input source has
greatly reduced the amount of pollutants discharged to the IRL (SJRWMD
2007). Public education initiatives have also increased public awareness
of the nutrient impacts of yard fertilizer runoff and septic system
Muck Removal and Preemption
A number of muck dredge-removal projects, both current and planned, will
augment the normal maintenance dredging of the Intracoastal Waterway (ICW) and navigational
channels within the IRL and will also remove large amounts of muck. Although dredging
can temporarily elevate turbidity and release trapped nutrients, removal
projects managed to minimize unintended side-effects will continue to
improve habitat quality in the estuary.
In addition to removing existing deposits, important steps are being taken
to reduce the input of new deposits. The primary sources of muck are poor
erosion control practices and decayed plant material. The installation of
stormwater sediment traps and the recent implementation of improved best
management practices for new construction has slowed the rate of
Several initiatives have been undertaken to address the biotoxin issues
affecting the lagoon (IRLNEP 2006). A Biotoxin and Aquatic Animal Health
Working Group was formed in 2005 to study current health issues affecting
lagoon fauna. The Florida Fish and Wildlife Conservation Commission's
Florida Fish and Wildlife Research Institute has also begun to look for a
connection between invertebrate disease and exposure to saxitoxin.
Additionally, an ongoing collaborative monitoring project conducted by the
University of Florida, the Florida Space Research Institute, and the
Florida Fish and Wildlife Research Institute is aimed at tracking the
occurrence and distribution of harmful algal blooms in the lagoon.
Brevard County Health Department. Undated. "Eat Puffer, You Will Suffer."
Public awareness poster. PDF document available online.
Duarte CM. 2001. Seagrass Ecosystems. pp. 254-268 in: Levin SL (ed.).
Encyclopedia of Biodiversity, Vol. 5. Academic Press, San Diego.
Florida Department of Environmental Protection (FDEP). 2003. Evidence of
Impairment: C-25 Canal (WBID 3163B) per Florida Impaired Waters Rule
62-303.330(4). Florida Department of Environmental Protection, Southeast
District. Ambient Water Quality Section, Port St. Lucie FL. 13 p.
Fish and Wildlife Research Institute (FWRI), Florida Fish and Wildlife
Conservation Commission. Undated. Red Tides In Florida. Available online.
Haddad KD. 1985. Habitats of the Indian River Lagoon. pp 23-28 in Barile
D. (ed.). Proceedings of the Indian River Resources Symposium. Florida Sea
Grant Project No. 84-28, Gainesville, Florida. 160 p.
Hanisak MD. 2002. Impacts of Reduced Salinity on Seagrasses in Indian River
Lagoon. Journal of Phycology, Volume 38, Supplement 1:15-16.
Haunert DE, and JR Startzman. 1985. Short term effects of a freshwater
discharge on the biota of the St. Lucie estuary, Florida. South Florida
Water Management District Resource Planning Department, Environmental
Sciences Division Technical Publication 85-1, West Palm Beach, Florida.
Hirama S and LM Ehrhart. 2007. Description, prevalence and severity of
green turtle papillomatosis in three developmental habitats on the east
coast of Florida. Florida Scientist 70:435-448.
Indian River Lagoon National Estuary Program (IRLNEP). 2006. Indian River
Lagoon Update. Volume XIV Number 1, Winter 2006.
Kenworthy WJ and DE.Haunert. 1991. The light requirements of seagrasses:
Proceedings of a workshop to examine the capability of water quality
criteria, standards and monitoring programs to protect seagrasses. NOAA
Technical Memorandum NMFS-SEFC-287, Beaufort, NC.
Morris LJ and DA Tomasko. 1993. Proceedings and conclusions of workshops:
Submerged aquatic vegetation initiative and photosynthetically active
radiation. St. Johns River Water Management District Special Publication
SJ93-SP13, Palatka, FL.128 p.
Reif JS, Mazzoil MS, McCulloch SD, Varela RA, Goldstein JD, Fair PA, and GD
Bossart. 2006. Lobomycosis in Atlantic bottlenose dolphins from the Indian
River Lagoon, Florida. Journal of the American Veterinary Medical
Saint Johns River Water Management District (SJRWMD). 2007. Indian River
Lagoon, An Introduction to a Natural Treasure. Saint Johns River Water
Management District. 36 p.
Steidinger KA Landsburg JH, Truby EW, and BS Roberts. 1998. First report of
Gymnodium pulchellum (Dinophyceae) in North America and associated fish
kills in the Indian River, Florida. Journal of Phycology 34:431-437.
Strom D, and M Thompson. 2000. Biological implications of stable salinity
gradients within the context of the St. Lucie Estuary, Florida. Florida
Department of Environmental Protection, Southeast District Water Quality
Program. 13 p.
Report by: J. Masterson, Smithsonian Marine Station
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Page last updated: October 1, 2008