Smithsonian Marine Station at Fort Pierce

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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 health.

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 here.

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 2000).

Stormwater Runoff

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.

Nutrient Input

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 great concern.

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 dolphin infections.

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 regional.

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.

Hydrology Initiatives

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 Everglades.

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 Abatement

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 discharge.

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 deposition.

Addressing Biotoxins

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.

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 Association 228:104-108.

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.

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