Thirty-seven sediment samples from the fresh/brackish water systems and the surrounding marine waters of the Ebro Delta have been analyzed for organic and inorganic carbon, carbohydrates, amino acids and lipids. The study of individual lipid components showed autochthonous and allochthonous contributions of organic materials to the system, namely higher plant residues, allochthonous soil-related components, macrophytes, unicellular algae and microbial residues. However, algal constituents are predominant in most sediments, suggesting that decomposition and remineralization of allochthonous organic matter, and subsequent enhancement of algal production, may be one of the major processes of the carbon cycle in the delta. The persistence of cycling intermediate and particularly labile compounds in the samples is constrained by environmental conditions of deposition. Accordingly, six depositional environments have been characterized (listed from more reducing to more oxic): the coastal lagoons, the bays, the river bed, the open sea area located around and far from the river mouth, and the coastal sandy sediments.