Abstract Certain organic molecules are potentially powerful tracers because of the specificity of their biosynthesis in different organisms, the adaptation of biosynthetic systems to environmental parameters, and their stability in recent environments. To assess the use of these molecules in estuarine systems for recording river and marine organic matter sources and sinks, the Krka estuary was chosen. This estuary is characterized by a marked stratification of waters, with closely associated fresh and marine planktonic populations and the presence of a halocline where both living and non-living organic material sinking from fresh waters accumulates. The compositions of sterols associated with particulate matter and present in the dissolved phase were determined in samples collected at three stations in May 1988. Analyses were performed by gas chromatography and gas chromatography/mass spectrometry. Differences were observed between sterol compositions obtained for river waters and marine waters. Sterol distribution patterns are discussed as possible criteria for distinguishing different organic matter inputs: terrestrial higher plants (24-ethylcholest-5-en-3β-ol); freshwater and marine phytoplankton, (27-nor-24-methylcholesta- 5, 22-dien-3β-ol, 24-ethylcholesta-5, 22-dien-3β-ol, 24-methylcholesta-5, 22, dien-3β-ol and 24-methylcholesta-5, 24(28)-dien -3β-ol); and sewage outfalls in the highly eutrophic zone off the city of Šibenik (5β-cholestan-3β-ol).