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 DOM was separated by reversed-phase chromatography and analyzed with ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The number and summed magnitudes of FT-ICR MS peaks, enriched in the microlayer, increased with increasing salinity along the estuary. The molecular hydrogen to carbon ratio (as a measure 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 estuary with the microlayer 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 underlying water. The redistribution of dissolved organic carbon within chromatographic fractions and the decrease in molecular size was 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 the microlayer. Molecular level investigation of estuarine surface microlayers will help to better understand the highly dynamic character of these systems, the accumulation of natural organic matter and anthropogenic pollutants and the role of surface microlayers for the sea-air energy exchange. © 2013 Elsevier B.V.