Stay in the know about wildlife, water quality, and ecosystems on Sanibel and Captiva Islands and in Southwest Florida
What is Colored Dissolved Organic Matter?
Visual representation of a Colored Dissolved Organic Matter (CDOM) plume surrounding the Sanibel Lighthouse. Photo from Sept. 29, 2025.
Have you ever wondered why the Caloosahatchee is brown? Have you noticed during the rainy season that the waters around Sanibel have turned from a beautiful azure to a murky, less-than-desirable shade?
Colored Dissolved Organic Matter (CDOM) is one of the water quality parameters impacting the color and clarity of the water. The SCCF Marine Laboratory monitors CDOM through its River, Estuary, and Coastal Observing Network (RECON). The RECON system currently consists of eight water quality monitoring stations throughout the Caloosahatchee River, and also in the estuary and Gulf.
What Exactly is CDOM?
CDOM is dissolved in the water and is a complex mixture of organic compounds from terrestrial plants, microorganisms, and stormwater runoff. Organic matter dissolved in the water appears brown, similar to brewing a cup of tea, and is most noticed in the lower estuary during the summer season when daily rainfall bring freshwater to the waters surrounding the barrier islands. Colored dissolved organic matter can also originate from marine sources such as from the sediments and mangroves in the lower estuary.
Most of the CDOM in the estuary is derived from terrestrial sources and is an important indicator of the amount of mixing of freshwater and marine water in the estuary. Subsequently, there is a negative correlation between CDOM with salinity (high CDOM, low salinity) and a positive correlation between CDOM and nitrogen. Nitrogen can be from human sources (e.g. fertilizer, animal waste) or from nutrient cycling that occurs in microorganisms when they are producing amino acids and proteins. Terrestrial plants produce complex organic compounds to deter grazing and other purposes which ends up in soils and eventually dissolved in the rainwater that falls throughout the watershed.
“The ebb and flow of the tide can extract CDOM from sediments, specifically mangroves. This runoff inevitably ends up in our local rivers and estuaries, bringing with it that unpleasant brown color,” said SCCF Marine Lab Research Assistant Rachel Wynn. “SCCF scientists liken it to brewing a cup of tea. You add tea bags, full of organic material, to steep in a cup of water. After a few minutes, the tannins from those tea bags have leached into your cup, the dissolved organic material now ‘staining’ the surrounding water.”
This process is most noticeable during the wet summer season, when the daily rain cells and storm events bring large quantities of stormwater to the clear waters around Sanibel.
“It’s almost as if the change occurs overnight,” Wynn said. “Driving over the Causeway one afternoon will feel like you’re driving in the Keys, and then with one significant downpour, the water will look like brewed tea.”
Damaging flows (>2,600 cubic feet per second) from Lake Okeechobee can also contribute to high CDOM in the estuary and bays.
CDOM plays an important role in aquatic ecosystems by attenuating light in the UV and blue spectrums, supporting benthic species that may be sensitive to light in those ranges, such as delicate coral reefs.
However, too much CDOM can have a negative impact to those same deeper environments. Too much CDOM can block light to submerged aquatic vegetation, limiting photosynthesis and ultimately inhibiting the first level of the trophic food web.
“As a resident or visitor to Sanibel you can help mitigate the increased CDOM pressure to our waterways by limiting fertilizer use on your lawns and always picking up pet waste,” Wynn said.
To take a deeper dive into the world of CDOM, a 2010 paper the Marine Lab published can be read here.
SCCF has been monitoring CDOM in Southwest Florida since 2007.
Other Factors Impacting Water Clarity
Water color and clarity can also be impacted by turbidity, which can increase with high winds and tidal shifts that re-suspend sediments, as well as Chlorophyll a, the most common pigment in phytoplankton (microscopic algae). Compared to turbidity and chlorophyll a, CDOM is the greatest contributor to decreased light availability.