Water Quality FAQ

SCCF uses science, education, and advocacy to protect water quality in Southwest Florida. Our Marine Laboratory, RECON sensor array, mangrove and oyster restoration programs, and environmental policy department all interface to help inform the public, water managers, and elected officials about water issues and solutions.

Find answers to some of our most commonly asked questions below.

What is the Caloosahatchee Estuary?

The Caloosahatchee is a 70 mile long river and estuary in Southwest Florida that runs from Lake Okeechobee to the Gulf of Mexico across the western two-thirds of Florida.

The historic Caloosahatchee was a curving river with its headwaters at a waterfall 2 miles east of today’s city of LaBelle. The waterfall and rapids were located on the western edge of Lake Flirt, the westernmost of a series of lakes and marshes that stretched to Lake Okeechobee. The marsh lands, west of Lake Okeechobee and east of Lake Flirt, were part of the Lake Okeechobee floodplain and historic western Everglades.

The Caloosahatchee means “River of the Calusa," and it was named after the indigenous Calusa who inhabited the region and used the river as an important trade route (Hatchee = Seminole for river).

Today, the Caloosahatchee is a highly managed canal controlled by three lock-and-dam structures dividing the upper 44 miles of the freshwater river into two freshwater sections that flow into the tidally influenced estuary west of the WP Franklin Lock and Dam, known as S-79 (structure 79). The placement of the western lock cut the estuary short by approximately 12 miles.

Freshwater feeds into the river from both Lake Okeechobee and the 865,063 acres that make up the Caloosahatchee watershed north and south of the river.

Unintended consequences of the alterations of the river have created problems with the volume, timing, and quality of the water in the river and estuary. The volume of water received from the watershed and the lake contribute to altered salinity conditions, increased nutrient concentrations, and decreased light availability. These changes in water quality can have negative effects on important indicator species such as oysters and seagrass.

The Caloosahatchee is home to, and designated critical habitat for, the federally listed, critically endangered smalltooth sawfish and the vulnerable Florida manatee. These species and their habitat have been negatively affected by changes in water flow and quality.

Why does the Caloosahatchee receive water from Lake Okeechobee?

The Caloosahatchee Estuary has a long history of development and a complex ecology that are inextricably linked to the water quality issues we face today.

In the late 1800s, in an effort to drain south Florida wetlands and provide a navigable boating route between Central and Southwest Florida, the Caloosahatchee river was artificially connected to Lake Okeechobee. The connection unintentionally resulted in flooding for downstream communities, as the water in Lake Okeechobee overwhelmed the river channel.

In time, the Caloosahatchee continued to be developed through a series of projects that dredged and widened the river, and three locks and dams were added for flood control and navigation. Now, the Caloosahatchee River and Estuary are part of a large system managed by federal and state entities in order to balance the needs between flood control, navigation, water supply and protecting the environment.

Historically, the natural flow of water to the Everglades started south of Orlando in the Kissimmee River which drained into Lake Okeechobee. During the wet season, water overflowed the southern banks of the lake to the Florida Bay in a slow moving shallow sheet, named “The River of Grass” by conservationist and author Marjory Stoneman Douglas.

Following a series of storms and two massive hurricanes in the 1920s that killed 3,000 people around the lake, Congress initiated a federal project to build a dike to contain the massive lake. The Herbert Hoover Dike was completed in the 1930s, and the historic water flow south out of the lake into the Everglades was cut off. The restricted flow resulted in increasing flows to the Caloosahatchee Estuary and destruction of one of the most unique habitats in the world: the Florida Everglades.

What affects Sanibel Island water quality?

Sanibel Island is home to beautiful beaches, mangrove and seagrass ecosystems, and diverse wildlife due to the preservation of 70% of land for conservation. However, the water surrounding Sanibel is heavily influenced by nutrients and runoff from the Caloosahatchee Estuary, which is connected to the largest watershed in Florida via Lake Okeechobee. It is part of a complex, highly managed system that is federally required to balance the needs for flood control, navigation, the environment, and water supply for agricultural and municipalities by the U.S. Army Corps of Engineers.

The Caloosahatchee Estuary has been artificially connected to Lake Okeechobee since the late 1800s and is now seasonally dependent on flows from Lake Okeechobee due to the intense development of the land around the formally winding, slow moving river. During the dry season, the estuary needs a minimum amount of flow in order to maintain a salinity gradient that supports thriving seagrass and oyster populations. During the wet season, most of the water that goes into the estuary comes from runoff along the Caloosahatchee watershed, which can cause tannin colored, nutrient laden water to enter our estuary. Excessive fertilizer usage and outdated septic and stormwater systems contribute to high nutrient loads throughout the watershed and get flushed into the estuary after it rains. In addition, there are too many times when the needs of agriculture are prioritized over the needs of the environment, and we are inundated with damaging high flows directly from the polluted waters of Lake Okeechobee. With these damaging flows comes high nutrient loads which results in devastating effects in our natural and human communities including macroalgae overgrowth, harmful algal blooms (red tide), low oxygen, seagrass die off, oyster mortality, fish kills, wildlife death, threats to human health, loss of tourism, and negative effects on the economy.

What causes the water to look brown?

The Caloosahatchee Estuary is home to five species of seagrass that require light for growth and survival. Seagrass is an indicator of water quality and provides important habitat in the Caloosahatchee Estuary. High turbidity, water color (CDOM), and chlorophyll all reduce the amount of light reaching the bottom where seagrass grows, a process called light attenuation. These three factors are influenced by tide, weather, flows from the watershed, and flows from Lake Okeechobee.

Important Water Clarity Parameters

  • Colored Dissolved Organic Matter (CDOM) is a natural component of Florida’s waters and is an organic component in the water that gives it a brown or orange color. This natural occurrence can be elevated when water cannot be filtered through a natural landscape. The predominant source of CDOM in our estuary comes from freshwater flows >1000 cubic feet per second (measured at the Franklin Lock & Dam) from the C-43 (Caloosahatchee) basin. Damaging flows (>2,600cfs) from Lake Okeechobee can also contribute to high CDOM in the estuary and bays. CDOM is the greatest contributor to decreased light availability compared to turbidity and chlorophyll.
  • Turbidity is caused by small particles such as decaying organic matter or minerals suspended in the water column that scatter light making the water appear cloudy. Turbidity can increase with high winds and tidal shifts that re-suspend sediments and is less associated with freshwater flow than color (CDOM) and chlorophyll.
  • Chlorophyll a is the most common photosynthetic pigment in phytoplankton (microscopic algae). This green pigment absorbs light and creates energy for the growth and reproduction of phytoplankton and is an indicator of primary production. Chlorophyll also causes light attenuation, but to a lesser extent than CDOM. In the upper parts of the estuary (closer to S-79, with fresher water) flow from the basin and the lake have little to no effect on chlorophyll, likely because higher CDOM blocks the light needed for phytoplankton growth and increased flows tend to push phytoplankton downstream. Damaging flows from the C-43 basin and Lake Okeechobee can increase chlorophyll in the lower estuary and bays. Chlorophyll is affected by nutrient concentrations as well as seasonal changes in light and temperature.

Other Factors Influencing Water Clarity

The tide can also affect water color and clarity at Lighthouse Beach Park where weekly aerial photographs are taken to demonstrate these effects. During a high tide, water from the Gulf of Mexico is pushed into Pine Island Sound which increases water clarity at Lighthouse Beach Park. During a low tide, water from the estuary pushes out into the Gulf of Mexico, decreasing water clarity. The angle of the sun on the water can also affect light attenuation. Low angles of the sun (like sunrise and sunset) will reduce the amount of light entering the water and can produce glare in photographs, which is why we take the aerial photos when the sun is close to the highest point in the sky (solar noon). High cloud coverage can also make the water appear less clear.

How can I tell if water is safe to swim in?

The water is not safe to swim in when there are harmful algal blooms such as red tide and blue green algae or when fecal coliform bacteria counts are high. Currently it is at the discretion of the Florida Department of Health to notify the public of health advisories, which typically involves putting up a sign and online notices, and to enforce rules on safety standards in public bathing places like beaches. View current advisories >>

In 2022, a bill that would make this mandatory instead of discretionary died in the senate (SB604: The Safe Waterways Act).

Brown and dark colored water on its own is not a public health issue and does not require beach closures or notices of health advisories — even though it's certainly not as nice as having clear, turquoise water.

SCCF releases a weekly aerial image of Lighthouse Beach Park, which on its own is not an indicator of the safety of the water for recreational activities. There may be an association between brown water and harmful algal blooms due to the nutrients associated with the runoff and releases, but it is not always the case.

How are the optimum flows for the Caloosahatchee Estuary determined?

The flow envelopes for the Caloosahatchee Estuary are determined based on the preferred habitat conditions of the Eastern oyster (Crassostrea virginica), freshwater tape grass (Vallisneria americana), and marine shoal grass (Halodule wrightii). Each species has a specific salinity tolerance, lives in different parts of the estuary, and provides important habitats that support a diversity of marine life throughout the estuary. The optimum flow envelope was determined so that within that flow range, each species would be within its preferred salinity range.

Tape grass lives in the upper estuary and prefers a freshwater environment. Salinities greater than 10 parts per thousand (ppt) can cause stress, and salinities greater than 15 ppt has lethal effects.

Oysters live in the middle estuary and prefer a salinity between 10 – 25 ppt. Prolonged exposure to low salinity associated with high flows can cause stress and mortality. High salinity can make oysters vulnerable to disease, predation, and mortality.

Shoal grass is a marine species of grass and can tolerate a range of salinity from 15 – 45 ppt. Shoal grass is vulnerable during very high flows that can reach the mouth of the estuary and reduce salinity to less than 15 ppt.

Knowing these tolerances, scientists and decision makers are able to use the 14-day average flow rate as a proxy for the optimum salinity in the estuary. This was developed in the RECOVER program using a model based on the relationship between flow and salinity using historical data over a 51-year period (1965 – 2015). When 14-day average flows are within the optimum flow envelope, the suitable habitat for each species is maximized.

Based on this model, the 14-day average optimum flow for the Caloosahatchee is 750 – 2,100 cubic feet per second (cfs) as measured at the WP Franklin Lock and Dam (S-79). The flow from S-79 is a combination of watershed runoff and Lake Okeechobee releases.

A 2024 publication on discharge volume and duration affects on seagrass in the Caloosahatchee suggests that prolonged flows of over 2,100 cfs average over 14 days lead to seagrass density declines and seagrass losses. 2100 cfs average over 14 days lead to density declines and seagrass losses.

Sometimes, the watershed flow alone is greater than 2,100 and other times, watershed runoff and Lake Okeechobee releases combine to cause damaging flows (> 2,600 cfs) that can lower the salinity to dangerous levels for oysters and shoal grass. Conversely, during the dry season, flow can decrease to less than 750 cfs, and if Lake Okeechobee is too low to make releases to the estuary, tape grass in the upper estuary can suffer.

To maintain a balanced flow regime year round, water storage projects such as the C-43 Reservoir are in the process of being built to store and treat excess water when flows are too high and release water when flows are too low. Additionally, the EAA Reservoir will increase storage capacity of water south of Lake Okeechobee and could reduce harmful flows the northern estuaries.

Why does the Caloosahatchee receive more flows from Lake Okeechoobee compared to the St. Lucie Estuary or the south?

The Caloosahatchee will typically have greater flows from Lake Okeechobee than the St. Lucie Estuary to the east. During some parts of the year, the Caloosahatchee Estuary will receive 100% of the flow from Lake Okeechobee.

Compared to flows going to the south, the Caloosahatchee will receive more or less flows from Lake O depending on the time of the year, water storage south of the lake, and weather forecasts. The U.S. Army Corps of Engineers makes decisions about flows from Lake Okeechobee based primarily on the lake operating schedule (LORS08) with considerations for recommendations by the South Florida Water Management District and various stakeholders.

For example, between May 25 and July 25, 2023 most of the water from Lake Okeechobee went to the Caloosahatchee Estuary. However, 94% of the water that was received was from the watershed, while only 6% of the water came from Lake Okeechobee. So, while we are receiving 100% of the flows from the Lake, the volume of the flow was minimal and had negligible impacts on the estuary compared to watershed flows.

One of the reasons the Caloosahatchee receives a greater volume of water than the St. Lucie Estuary is because the RECOVER performance measure for salinity and the ecology of each system requires different flows. The Caloosahatchee River and Estuary is larger than the St. Lucie Estuary, and the Caloosahatchee needs more freshwater in order to maintain a salinity gradient that supports a diversity of wildlife including submerged aquatic vegetation, seagrass, and oysters. The St. Lucie Estuary is smaller and requires less water to maintain a salinity gradient. All of the freshwater it needs can be provided by its own watershed and prefers to never get water from Lake Okeechobee. The massive annual summer algal bloom on the Lake also prevents flows from the Lake to the St. Lucie. Their Lock and Dam structure (S-80 in Port Mayaca) is situated in an area directly on the Lake, and our Lock and Dam structure (S-77 in Moore Haven) is separated from the Lake by a large marsh. Although that does not always prevent blue-green algae from blooming near our structure, it is more protected.

The EAA typically doesn’t need flow from Lake Okeechobee during the wet season because they get enough water from rainfall. The agriculture industry is protected from having too much or too little flow. That is largely politically motivated and protected by law in some cases. Moving water south towards the Everglades can be hindered by storm water treatment areas that have limited capacity to move clean water south to the Everglades and the Water Conservation Areas.

There are many times that the Caloosahatchee receives a proportionally larger volume of flow than other outlets simply because we have a greater capacity to receive large flows based on the engineering of the system. When flows are too high for too long, there can be damaging effects on our ecosystem.

How will Everglades restoration projects affect the Caloosahatchee?

The goal of the Comprehensive Everglades Restoration Project (CERP) is to provide greater storage and treatment of water to improve the quantity, quality, timing, and distribution of water throughout the Everglades system.

The C-43 Reservoir will store 55 billion gallons of water on 10,700 acres of land adjacent to the river in Hendry county. During the wet season, excess flows from basin runoff and regulatory releases can be stored and treated to remove harmful algae and nutrients. Then, during the dry season, clean water from this reservoir can be used to provide beneficial flows to the estuary. Construction for the project started in 2017 and is expected to be fully operational by 2026.

The EAA Reservoir will store 78 billion gallons of water south of the lake in order to reduce discharges from Lake Okeechobee to the northern estuaries. This project will also include a Stormwater Treatment Area (STA), which is a constructed wetland used to improve water quality by reducing nutrients and sediments. The EAA reservoir should be complete by 2032.

Can the system be changed back to pre-development conditions so the Caloosahatchee and St. Lucie are no longer connected to Lake Okeechobee?

After the massive engineering changes done to the system — starting with dredging canals in the 1880s and subsequent massive development of the region — changing the system back is not a viable option. Many areas in South Florida would become uninhabitable due to flooding and high nutrients in the water would not allow the Everglades ecosystem to persist, among other negative impacts.

Instead, the state is moving forward with the Comprehensive Everglades Restoration Program (CERP), which includes over 60 projects intended to work together to improve quantity, quality, timing, and distribution of water in South Florida. CERP is not a panacea, but it will help reduce the amount of water that goes to the Northern Estuaries and increase the volume that goes to the Everglades.

What prevents a drawdown of lake levels before the rainy season in some years?

Lake Okeechobee depth increases throughout the rainy season due to increased precipitation and greater inflows from the Kissimmee Chain of Lakes to the north.

During the dry season, lake levels decrease from increasing evapotranspiration (water evaporating form the surface of the lake), increased flows to the Everglades Agricultural Area (EAA) south of the lake, and beneficial releases to the Caloosahatchee Estuary.

This cyclic increase and drawdown of the lake mimics the lake’s natural process of increasing and decreasing depth throughout the year. Sometimes, an appropriate drawdown of the lake during the dry season, such as in 2023, is difficult due to other environmental conditions such as red tide. When there's an intense red tide bloom in the Gulf of Mexico during dry season, high volume discharges full of nutrients from Lake Okeechobee can intensity and prolong the red tide blooms. If the lake is too high, this can create a conflict between the need to reduce lake levels before the dry season and to protect the downstream communities from red tide blooms.

This scenario occurred in 2023 after lake levels were unseasonably high after Hurricane Ian. Red tide blooms plagued the coast and Lake Okeechobee releases were kept at ecologically beneficial levels to the Caloosahatchee, which stymied the reduction of Lake levels during the dry season. The lake was well above the preferred 12-foot level during the start of the rainy season on June 15 at 14.09 ft. By this point, increasing sunlight and temperatures had begun to fuel a bloom-green algal bloom on Lake Okeechoobee, which further prevented releases from the lake to the northern estuaries.

Another reason to avoid high releases in the late wet season are to avoid negative effects of low salinity on oysters and new oyster recruits. Sudden decreases in salinity can have negative impacts on adult oysters, causing them to close their valves and reduce their feeding rates. Low salinity also reduces growth rates in oysters as well as the development and recruitment of larval oysters. Late summer is the time of year when oyster reproduction is increasing, and the additional stressor of high temperature can exacerbate the effects of low salinity. Avoiding large releases late in the wet season can promote a stable salinity gradient for the reproduction and recruitment of new oysters.

What are the ecological consequences of Lake Okeechobee being too high?

High lake levels are damaging to Lake Okeechobee's submerged aquatic vegetation (SAV) and emergent plants in the littoral zone (area with aquatic plants on the shoreline) of the lake.

This vegetation provides important habitat for young-of-the-year (fish born in the last year) and juvenile bass, and multiple years of high lake levels can have devastating effects on the bass fishery of Lake Okeechobee.

Once SAV and emergent plants are damaged, it can take several years for them to recover if conditions are favorable.

If flows are in the optimal range, why am I seeing dead eel grass washing up on the beach?

When seagrass growth rates increase in the spring, older blades slough off at about the same rate, and some species actually die back in summer from the heat.

What is red tide?

Karenia brevis is a single-celled organism belonging to a group of algae called dinoflagellates. Large concentrations of this organism, called red tide blooms, can discolor water red to brown, giving it its name. Karenia brevis occurs in marine and estuarine waters of Florida and typically blooms in the late summer or early fall.

Blooms develop offshore and are brought inshore by currents and winds. Karenia brevis produces neurotoxins called brevetoxins that can sicken or kill fish, seabirds, turtles, and marine mammals. Toxins can also affect humans, causing respiratory irritation if aerosolized toxins are inhaled, skin and/or eye irritation by contact, or shellfish poisoning if shellfish contaminated with toxins are consumed.

Learn more >>

How does red tide affect human health?

Red tide can affect human health primarily through breathing in the toxins or through the consumption of contaminated shellfish.

Those with preexisting respiratory conditions should avoid breathing in red tide toxins if possible. Wearing a mask can decrease the symptoms. Shellfish harvesting closures occur when the abundance equals or exceeds 5,000 cells per liter. Fish kills occur at levels exceeding 10,000 cells per liter.

Shellfish Poisoning
Consuming shellfish during red tide can lead to Neurotoxic Shellfish Poisoning, which can include symptoms of abdominal pain, nausea, vomiting, diarrhea, and a prickling sensation in the mouth or other areas of the body. At background levels (0 - 1,000 cells per liter), no effects are expected to occur to human health. Once the concentration exceeds 1,000 cells per liter, the effects on the respiratory system get progressively worse as the concentration increases.

Call the Florida Department of Health Poison Hotline at 800-222-1222 with questions related to the health impacts from Red Tide.

If you experience symptoms related to red tide, these are the ICD-10 Codes to request that medical professionals use to help the CDC and Florida Department of Health track public health impacts.

  • T65.82 Harmful Algal Bloom (HAB) exposure in general
  • T65.84A - Initial HAB exposure - (Red Tide or cyanotoxin from blue-green algae)
  • Z77.121 - After-the-fact exposure, including longer-term effects from contact with HABs or toxic algae blooms
How does red tide affect wildlife?

Karenia brevis produces toxins called brevetoxins that affect various marine animals, including zooplankton, fish, and crustaceans. These toxins can accumulate and persist in the ecosystem, eventually transferring to larger animals like birds, sea turtles, and marine mammals.

Long after a red tide bloom stops occurring, the toxins that have accumulated in the food web (in seagrass, fishes, and other marine organisms) linger.

Birds that eat fish or crustaceans with toxins still in their systems end up getting red tide poisoning, also called toxicosis. Sick birds can appear lethargic and wobbly, and often display little fear of humans. 

How to spot and help birds affected by red tide>>

If you see a sick or injured bird near Sanibel or Captiva, please contact CROW at 239-472-3644 EXT. 222

Sea turtles can also become affected by red tide poisoning and will display symptoms including swimming in circles, head bobbing, lethargy, and jerky movements. If you find a sea turtle stranded or displaying these symptoms in the water, please call SCCF's Sea Turtle Hotline at at 978-728-3663.

The longer we remain red tide free, the more the effects on wildlife diminish.

How are satellites used to detect red tide and blue-green algae?

Remote sensing of red tide and blue green algae blooms is made possible through the use of satellites that detect the pigment chlorophyll in algae that is responsible for photosynthesis. Satellites orbit Earth up to twice daily and are able to detect the wavelengths of light the algal pigments reflect.

Remote sensing is good for identifying when and where large blooms occur but cannot be used to identify the species of algae that is blooming. When a bloom is detected using remote sensing, scientists can collect samples in the field and identify the dominant algal taxa that is responsible for the bloom.

Once it's confirmed through field observations that an algal bloom is being caused by the red tide forming species, Karenia brevis, it's likely that it is the dominant species throughout the detected region.

An addition algal pigment, phycocyanin, found in blue-green algae, is used to differentiate cyanobacteria from other algae by a method called the Cyanobacteria index.

A mixture of remote sensing and field observations gives us the best indication of the extent of a bloom, and which species are causing it. To learn more about remote sensing click here.

What can I do to help improve water quality?

The biggest thing you can do to improve water quality is to use your voice to spread awareness of the issues, advocate for policies that improve water quality, and fight against policies, legislation, and land use changes that can be detrimental to water quality. You can do this by voting for local and state positions that care about these issues, staying up to date with SCCF’s environmental policy efforts, including our legislative priorities and legislative tracker, and by signing up for our Action Alerts.

You can also incorporate changes into your life, such as using native plants in your landscape and minimizing the amount of turfgrass on your property.

Native plants do not require fertilizer or as much (if any) irrigation and create a friendly environment for wildlife such as birds, butterflies, and other important pollinators. Visit SCCF's Native Landscapes & Garden Center >>

Pet waste is a big contributor to nutrients in storm water runoff, so make sure to pick up after your pets on their walks. Make sure the stormwater drains on or near your property are clear of debris to make they are functioning efficiently. Don’t throw cigarette butts on the street where they can end up in waterbodies causing harm to fish and birds. Maintain your car and regularly check for leaking fluids.

Use fertilizers on your landscape responsibly. Applications are only needed once or twice a year and established landscapes can use low phosphorous fertilizers. Never apply fertilizer before rain is expected, the fertilizer will be washed off the landscape and into the surrounding water bodies, and your yard will not get the fertilizers it needs. When it come to fertilization, less is more! Don’t waste time or money on overfertilizing your yard at the expense of the environment and your wallet. You can also test the soil in your yard to determine if fertilizer is needed.

How can I stay informed on regional water quality conditions?

Water Conditions Tracker
SCCF's weekly water conditions tracker provides a quick snapshot of conditions around Sanibel and Captiva Islands. It also gives insight into how the complex and dynamic system of the Caloosahatchee estuary works by distilling scientific information in a simple and easy-to-understand way.

Subscribe now >>

RECON: Continuous Data
SCCF monitors water quality through the River, Estuary, and Coastal Observing Network (RECON), an array of water quality sensors deployed throughout the Caloosahatchee watershed. You can access data in real time at recon.sccf.org.

Action Alerts
Using science, SCCF's Environmental Policy team helps inform the public, water managers, and elected officials about water quality issues and what can be done to improve them. The team often enlists voices of the public to help advocate for better water quality. 

Sign up for action alerts >>

Social Media
Be sure to follow SCCF on social media on Instagram, Facebook, and X at @sccf_swfl. 

Water Quality News