In Phase I of the FCE-LTER project, scientists studied the accumulation of organic matter – or nutrient-containing compounds derived from living things – in the estuarine ecotones. Organic matter, which occurs in the form of dissolved organic matter or in clumps known as floc, is an important component of ecosystems, providing nutrients to plants and increasing their productivity, or the amount of living material. Numerous primary consumers, such as small fish and shrimp, rely on floc as a primary food source.

In the estuarine ecotones, organic matter can be produced locally as plant matter decays, or it can be delivered by upstream freshwater, groundwater, and ocean water. In Phase I, researchers wanted to find out whether the sources of organic matter differ between the Shark River Slough/Gulf of Mexico ecotone and the Taylor Slough/Florida Bay ecotone and whether patterns of organic matter delivery and accumulation would change once restoration projects that increase freshwater flow are implemented. They believed that an increase in freshwater flow would lead to an increase in organic matter accumulation, which would, in turn, lead to increased productivity.

In addition to examining the effects of freshwater flow on organic matter, FCE-LTER researchers studied the impacts of abiotic factors, such as sea level rise due to climate change and storm deposition, on organic matter dynamics.