Introduction to Harmful Algal Blooms (HABs) in South Carolina Freshwater Systems

Harmful algal blooms (HABs) occur when algal communities and cyanobacteria dominate water bodies or produce toxins or other compounds that can cause taste or odor issues in water and negatively impact the health of aquatic ecosystems. Although they can occur in marine and freshwater environments, this publication provides an overview of freshwater systems HABs (i.e., lakes, reservoirs, streams, rivers, and ponds) and details the causes and effects, detection mechanisms, and monitoring approaches in South Carolina. The information benefits researchers, Cooperative Extension personnel, and community members interested in understanding and monitoring HABs.


Both lentic (stagnant) and lotic (flowing) aquatic systems are viable habitats for a wide range of micro and macro-organisms that collectively contribute to ecosystem dynamics and health. Algae and cyanobacteria naturally occur at low levels in surface waters and play an important role as primary producers in aquatic ecosystems.1 Algal bloom refers to the temporal and spatial accumulation of phytoplankton in general or a single species in an aquatic environment.2 According to the US Environmental Protection Agency (EPA), HABs refer to “overgrowths of algae in water” (figure 1) that may be capable of producing toxins or other problematic compounds, contributing to taste and odor issues in drinking water, and causing harm to the environment, which can in turn, damage the economy.3 Although some algal blooms may not be toxic, the large biomass of HABs can impede the use of water and impact the health of other aquatic organisms.

The mechanisms of toxin-producing compounds are not fully understood, so it can be challenging to characterize blooms based on toxicity alone.1 The compounds produced vary by algal species and exhibit different effects on aquatic ecosystems. Increased understanding of the complex interrelationships between factors enhancing HABs and their detrimental impacts on humans, livestock, drinking water, the economy, and aquatic environments is critical to determining appropriate prevention, management, and monitoring actions.

A pond with a large portion of the surface covered by a bright green algal bloom.

Figure 1. A pond affected by harmful algal bloom. Image credit: SC Department of Health and Environmental Control (SCDHEC).

Types of Algae

Algae reside primarily in aquatic environments, though certain species inhabit wet soils, moist rocky areas, and even livestock troughs.4 Most algal species are autotrophic, obtaining energy and nutrients from the sun. A few algal species also possess the ability to be heterotrophic, consuming other organisms for energy and nutrients.5

Chlorophyta, Rhodophyta, and Phaeophyta are large macroscopic algae visible in coastal waters, lakes, and ponds.6 Phytoplankton are small algae that are vast in population and collectively generate most of the Earth’s annual oxygen.4 Phytoplankton primarily include diatoms (Bacillariophyta), dinoflagellates, and cyanobacteria (blue-green algae), and other species also exist in marine and freshwater systems.4 Diatoms generate about 20% of oxygen produced each year on the planet and contribute between 40% to 45% of the total production of organic compounds in the ocean. They play a vital role in removing carbon dioxide from the atmosphere due to their large cell size and rapid sinking rate.7 Dinoflagellates are algae with chloroplasts surrounded by three membranes (rather than two); they also have two flagella, slender thread-like structures that allow them to swim. Both marine and freshwater dinoflagellates have complex feeding habits, with some species autotrophic and others heterotrophic.8,9 Dinoflagellates form dense blooms of about ten million to one hundred million cells per liter in the presence of high levels of nitrates and phosphates and are often called red tide blooms.10

Cyanobacteria behave similarly to and are often referred to as “algae,” although they are technically bacteria. These organisms utilize sunlight to make their food and proliferate rapidly in warm and nutrient-rich environments (high in phosphorus and nitrogen). Many cyanobacteria species are dominant in freshwater, fix nitrogen (convert nitrogen from the atmosphere to nitrogen compounds useful for biochemical processes), and serve as food for other aquatic organisms. Water bodies impacted by cyanobacteria often turn a bright green color; they can also turn a reddish color during blooms if excess red pigment (phycoerythrin) conceals the blue-green pigment (phycocyanin).4 Cyanobacteria are responsible for the most frequent and severe blooms in freshwater systems and are referred to as CyanoHABs, which could be large or attached to rock surfaces and freshwater sediments.

Causes of HABs

HABs are caused by the rapid proliferation of cyanobacteria capable of producing toxins or algal species that threaten aquatic ecosystems due to their biomass. Enabling conditions include

  • Warm water temperature (> 77oF)11
  • High-intensity sunlight12,13
  • Slow-moving water14,15
  • Elevated nutrient levels10,11

In freshwater ecosystems, HAB dynamics are affected by complex physical, chemical, biological, hydrological, and meteorological conditions. The rate of biochemical reactions involving algal growth is often triggered by warm water temperature. Intense sunlight also increases the photosynthetic abilities of most HAB species. Slow-moving water increases nutrient retention time in reservoirs and triggers rapid nutrient utilization, which can lead to accelerated growth. Nitrogen and phosphorus are the primary nutrients of interest, and requirements vary by algae species. Nutrients come from various sources such as fertilizer, soil erosion, agricultural farmlands, sewage effluents, and industries.14 Elevated nitrogen and phosphorus concentrations highly influence the occurrence of blooms.10 The presence of certain species of algae may be influenced by the relative ratio of nitrogen or phosphorus to silicate.14 Changes in N:P ratio due to variations in nutrient loadings have sometimes been related to the increased abundance of certain HAB species.14 Heavy rainfall events after periods of extended drought often trigger the growth of HABs due to the rapid increase of nutrient loading into water bodies.16

Less extreme rainfall events that allow continued stratification (layers of warmer water over cooler water) of a reservoir often increase the intensity of an algal bloom; because the algal communities can rapidly grow and absorb introduced nutrients. Drought conditions lengthen the time water remains within a pond or lake, encourage thermal stratification, and decrease the depth of the mixed layer resulting insufficient nutrient mass present to support an algal bloom.16

Location of Freshwater HABs

Waterbody that appears green due to algae growth.

Figure 2. Algal bloom event in Boyd Millpond. Image credit: Reedy River Water Quality Group.

Freshwater bodies such as rivers, lakes, and ponds are often breeding grounds for HABs. Due to increased enabling conditions (discussed above), algal blooms occur more frequently in ponds and lakes (figure 2). Stormwater ponds are used as Best Management Practices (BMPs) to improve stormwater quality by detaining runoff during storm events for an extended period to allow pollutant settling before cleaner water is discharged.17 Over time, stormwater ponds fill with sediment and may have additional conditions, such as elevated nutrient levels, conducive to excess aquatic plant growth. In the presence of other enabling conditions, rapid algae proliferation can occur, and the pond may develop unhealthy or toxic conditions. Especially after extreme storms, when lakes and ponds receive runoff and contaminants from agricultural and urban sources, nutrient levels may spike and accelerate the rapid proliferation of aquatic plant growth, including algae and cyanobacteria.18

Effects of HABs in South Carolina

The effects of HABs on human health and the economy are very detrimental, locally and globally.19 Impacts are both direct through toxin production and indirect through the creation of hypoxic (low oxygen) conditions. Low oxygen conditions develop during the decomposition of dead algal cells. This lack of oxygen leads to an imbalance in the ecosystem, affecting recreational opportunities, animal mortalities, economic value through tourism, and environmental quality endpoints.20

Large, freshwater algal blooms can disrupt ecosystems and interfere with water use through their high biomass and actual or potential toxin production.21 Various species of algae in freshwater exhibit different effects on the deterioration of water quality. Cyanobacteria are a widely studied and problematic type of HAB in freshwater in the United States and worldwide. Toxin production by cyanobacteria can deteriorate water quality, affect human health, and damage animal health or cause animal mortalities.22 Over 4,000 reports on HAB-related outbreaks were received by environmental and health departments across the United States between 2007–2011,23 with significant impacts on the nation’s economy.24 Toxin exposure routes for humans and animals include drinking contaminated water, feeding on exposed aquatic animals, ingesting contaminated nutritional supplements, ingestion of algal materials, skin contact with contaminated water, and licking contaminated furs.25,26

Several HAB-related issues in South Carolina have been reported to the South Carolina Department of Health and Environmental Control (SCDHEC). For instance, HAB-related toxin effects such as fish kills or taste and odor issues were reported in Lake Wateree,27 Walton Pond, Broad Creek landing in 2018, and Goose Creek Reservoir in 2019, 2020, and 2021. The SCDHEC issued recreational advisories for Lake Wylie, Lake Whelchel, Lake Edgar Brown, and Lake Rabon in 2020 and 2021 (based on EPA recreational standards for algal toxins after detection of expanding HABs).28 On a separate occasion, in 2021, extensive blooms of Lyngbya wollei—a type of cyanobacteria that can produce cyanotoxins—were also reported in various areas on Lake Wateree.29 These frequent HAB occurrences may be due to enabling conditions escalated by nutrient pollution in the water bodies.

HAB-related toxins or cyanotoxins can be classified based on toxicological effects into hepatotoxins (damage the liver), neurotoxins (damage, destroy, or impair the nervous system), and contact irritants (skin rashes).30 Hepatotoxins include microcystis and cylindrospermopsin, while neurotoxins include saxitoxin and anatoxin. Reported impacts after human ingestion of cyanotoxin-contaminated water include gastrointestinal and liver inflammation, drowsiness, pneumonia, incoherent speech, respiratory paralysis, and possibly death.27

Monitoring and Detection of HABs

HAB monitoring is essential to protect human, animal, and ecosystem health. Monitoring helps to identify blooms and inform the public when to avoid waterbodies. Monitoring approaches adopted include remote sensing, in-situ (on-site monitoring) and image-based assessments, molecular approaches, and laboratory analysis of water samples.31–33

Remote sensing approaches utilize satellite imagery to quantify chlorophyll biomass and organic carbon based on the water’s color and are often used for monitoring blooms in the ocean. The most frequent satellite data used for this purpose are Sea-viewing Wide Field-of-view Sensor (SeaWiFS), Moderate Resolution Imaging Spectroradiometer (MODIS), Medium Resolution Imaging Spectrometer (MERIS), Visible Infrared Imaging Radiometer Suite (VIIRS), and the ocean and land color instrument (OLCI) sensor on Sentinel-3.34 HAB monitoring with satellite data involves visual interpretation of discoloration in images and spectral analysis of distinctive characteristics for HABs using software like Sentinel Application Platform (SNAP).35 However, remote sensing methods are limited by an inability to monitor HABs beneath water surfaces since reflectance values are often based on images capturing the water’s surface. Cloud interference can also blur images, thereby compromising the clarity and integrity of images.36

Water quality sampling equipment, such as a cooler, boots, and plastic containers.

Figure 3. Sampling equipment for in-situ and laboratory analysis of HABs. Image credit: Reedy River Water Quality Group.

In-situ sensing methods entail using single to multispectral fluorometers, absorption sensors, and particle size analyzers to quantify the features of organisms in a water body (figure 3). Various technologies to measure phytoplankton are discussed in Lombard et al.37 Image-based approaches involve image capturing equipment like FlowCAM, Imaging FlowCytobot (IFCB), and CytoSense to detect and monitor HAB species. These instruments use fluid principles based on flow cytometry and video technology to generate high-resolution images of particles in the water body for proper characterization.

Molecular,31 microscopic, and laboratory-based analytical processes33 can also quantify HAB cells. Cyanotoxin levels can be detected using biological assays, including whole-organism bioassays, biochemical assays, and immunological assays,38 such as the Enzyme-Linked Immunoassay (ELISA) test. Analytical methods such as capillary electrophoresis (CE), nuclear magnetic resonance (NMR), and mass spectrometry (MS) coupled with liquid chromatography (LC) or gas chromatography (GC), and matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TsOF-MS) can also be used for detection of cyanotoxins.38 However, these methods are limited by the inability to cover a large spatial extent and are often used collectively with remote sensing approaches as part of a robust monitoring program.

South Carolina Cyanotoxin Monitoring and Reporting

In 2018, SCDHEC launched the SC Cyanotoxin Distribution Project and began routinely monitoring for cyanotoxins in various freshwaters across the state and started monitoring saltwater influenced sites, such as estuaries, in 2020.27 The program goals are to establish a baseline of cyanotoxin distribution, monitor levels throughout the year, identify potential reservoirs of concern, and determine potential risks of the water for drinking, recreation, and aquatic life.27 The project includes routine monitoring of strategic water bodies and event-driven responses. The SCDHEC prioritizes event-driven response sampling to publicly accessible water bodies popular for public recreation. If a single sample exceeds the standard for either microcystin or cylindrospermopsin, SCDHEC will issue a swimming advisory that remains in effect until future sampling results are below the standard.39 If three swimming advisories are issued for a waterbody within a three-year assessment period, SCDHEC may include the waterbody impairment on the 303(d) list,39 which is the state’s list of impaired and threatened waters based on the Clean Water Act (CWA).

The SCDHEC provides real-time information regarding cyanotoxin monitoring and reports advisories through the Algal Bloom Monitoring interactive online map. HABs can also be prevented by reducing point and nonpoint source nutrient loadings (e.g., reducing fertilizer usage and proper sewage disposal and treatment). The reader is encouraged to consult the fifth article in the additional resources section for further information on HABs prevention.

Standards for Cyanotoxins, Chlorophyll a, and Nutrients in South Carolina

Criteria exist for cyanotoxins in both drinking water and recreational water to help protect public health. For drinking water, the US Environmental Protection Agency has identified a 10-day health advisory criteria for microcystin and cylindrospermopsin concentrations of 1.6 μg/L and 3.0 μg/L, respectively, in school-age children,27,40 which can be measured from their blood serum and urine.41 These concentrations are lower for children under six years old since the risks associated with contaminated water are higher. In 2020, South Carolina adopted primary recreation standards applicable to recreational waters throughout the state for select cyanotoxins, including microcystins and cylindrospermopsin (table 1).39 South Carolina’s regulations limit the discharge of nutrients, including but not limited to phosphorus and nitrogen, to waters of the State through a narrative standard that applies to all freshwaters and a numeric standard applicable to lakes of forty acres or more (table 1).39

Table 1. South Carolina water quality standards relevant to Harmful Algal Blooms (adapted from SCDHEC Regulations and Standards).39

Water Quality Parameter Applicability SC Water Quality Standard
Blue Ridge Piedmont and

Southeastern Plains

Middle Atlantic

Coastal Plains

Microcystin Freshwater for recreational use 8 µg/L
Cylindrospermopsin Freshwater for recreational use 15 µg/L
Nutrients Freshwaters Discharges of nutrients from all sources, including point and nonpoint, to waters of the State shall be prohibited or limited if the discharge would result in or if the waters experience growths of microscopic or macroscopic vegetation such that the water quality standards would be violated, or the existing or classified uses of the waters would be impaired.
Chlorophyll a Lakes 40 acres

or more

10 µg/L 40 µg/L 40 µg/L
Phosphorus, Total Lakes 40 acres

or more

0.02 mg/L 0.06 mg/L 0.09 mg/L
Nitrogen, Total Lakes 40 acres

or more

0.35 mg/L 1.50 mg/L 1.50 mg/L


The monitoring, modeling, and management of HABs is critical due to their direct and indirect effects on human health, animals, ecosystems, and the economy. HABs that produce large biomass can interfere with water usage and threaten aquatic ecosystems, while HABs that produce cyanotoxins can cause life-threatening issues to humans and animals. Cyanotoxins have been reported in aquatic ecosystems across the United States and specifically in South Carolina freshwater systems. The SCDHEC developed a HAB monitoring and reporting program to help protect people in South Carolina from HABs. The complex interactions between HABs (particularly cyanobacteria enabling conditions such as elevated nutrient levels in slow-moving warm water), and the diversity of algae species that cause blooms, necessitate the adoption of holistic approaches for their management. Strategies such as reducing point and nonpoint source nutrient loadings through various approaches are essential to reduce the occurrence of HABs and production of cyanotoxins effectively.

Additional Resources

Ponds in South Carolina

Recreational Ponds in South Carolina

An Introduction to Stormwater Ponds in South Carolina

Pond Weeds: Causes, Prevention, and Treatment Options Carolina

Cyanobacteria: Understanding Blue-Green Algae’s Impact on Our Shared Waterways

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