Lignin is found only in vascular plant tissues, hence monitoring of lignin in aquatic environments is important in the determination of the sources and fate of terrestrial organic matter (OM). Concentrations of lignin-derived phenols provide an estimate of the amount of terrestrial OM in a system. Other lignin parameters such as the ratios of syringyl to vanillyl (S/V) and cinnamyl to vanillyl (C/V) phenols provide information on vegetation sources; and the ratios of vanillic acid to vanillin, (Ad/Al)v, and syringic acid to syringaldehyde, (Ad/Al)s, indicate the degradation stage of lignin materials. Concentrations of lignin-derived phenols were determined for the surface and subsurface sediments of a Scottish sea loch, Loch Creran, using a CuO oxidation method. In order to achieve the highest methodological efficiency, a series of validation experiments for each procedural step were carried out. As a result, several procedural steps were optimized. It was found that a lower oxidation temperature resulted in higher product yield and the duration and temperature of the silylation step have no effect on the outcome of the process. Studies of seasonal variations of lignin parameters showed that the occasional increase in lignin content in sediment trap samples was attributable to materials discharged from River Creran and the incoming water from the direction of Creagan bridge. The flow regime caused resuspension of surface sediments and entrainment of lignin materials into the water column. Lignin parameters exhibited more significant trends across an axial transect of the loch (from the head to mouth). Total lignin content decreased and the C/V ratios increased from upper to lower Loch Creran as these lignin materials were transported further down the loch and were subjected to hydrodynamic sorting processes.