Sea-surface microlayers and the corresponding underlying waters of the karstic Krka Estuary (Croatia) were studied with respect to optical and molecular properties of dissolved organic matter (DOM). Solid-phase extracted DOMwas separated by reversed-phase chromatography and analyzedwith ultra-high resolution Fourier transformion cyclotron resonance mass spectrometry (FT-ICRMS). The number and summedmagnitudes of FT-ICR MS peaks, enriched in themicrolayer, increased with increasing salinity along the estuary. The molecular hydrogen to carbon ratio (as ameasure of polarity) of enriched compounds was higher for the low salinity samples than for a high salinity marine station, which we propose is a consequence of a salt-mediated separation mechanism. Absorption and fluorescence of all samples decreased along the estuarywith themicrolayer samples showing higher absorption than the underlying water. Chromatographic and FT-ICR MS data revealed a distinct shift towards a smaller molecular size in the microlayer compared to the underlyingwater. The redistribution of dissolved organic carbonwithin chromatographic fractions and the decrease inmolecular sizewas interpreted to result from photo-degradation and/or microbial reprocessing. Collision induced dissociation of selected FT-ICR MS mass peaks revealed the presence of sulfur containing anthropogenic surfactants enriched in themicrolayer. Molecular level investigation of estuarine surfacemicrolayers will help to better understand the highly dynamic character of these systems, the accumulation of natural organicmatter and anthropogenic pollutants and the role of surface microlayers for the sea-air energy exchange.