Nine sediment samples were collected from a transect that extends from the central section of the Everglades National Park, through the Harmey River out to the Florida Shelf, to determine sources and fate and transport characteristics of the organic matter in this aquatic environment. Samples representative of the area plant communities such as mangroves, periphyton, sawgrass, and seagrass were also collected studied. All samples were analyzed for their lipid composition and a variety of biomarkers for the different sources of organic matter were identified. Preliminary results show that the molecular marker approach can differentiate between mangrove, periphyton and seagrass organic matter imputs. In addition a C-25 bicyclic diene (C25:2:2) commonly thought to be a marine biomarker was identified in the samples with predominantly marine influence, while the ketone fraction was found very useful in the assessment of seagrass imputs. Clear trends of organic matter source changes were observed throughout the sampling transect.