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Abstract. Sedimentary records of lipid biomarkers such as leaf wax n-alkanes are influenced by not only ecosystem turnover and physiological changes in plants but also earth surface processes integrating these signals into the sedimentary record, though the effect of these integration processes is not fully understood. To determine the depositional constraints on biomarker records in a high-altitude small catchment system, we collected both soil and stream sediments along a 1000 m altitude transect (1500–2500 m a.s.l.) in the Areguni Mountains, a subrange of the Lesser Caucasus Mountains in Armenia. We utilize a treeline at ∼ 2000 m a.s.l., which separates alpine meadow above from deciduous forest below, to assess the relative contribution of upstream biomarker transport to local vegetation input in the stream. We find that average chain length (ACL), hydrogen isotope (δD) and carbon isotope (δ13C) values of n-alkanes are significantly different in soils collected above and below the treeline. However, samples collected from the stream sediments do not integrate these signals quantitatively. As the stream drops below the treeline, the ACL, δD and δ13C values of n-alkanes preserved in streambed sediments reflect a bias toward n-alkanes sourced from trees. This suggests that either (1) there is minimal transportation of organic matter from the more open vegetation at higher elevations or (2) greater production of target biomarkers by trees and shrubs found at lower elevations results in overprinting of stream signals by local vegetation. Though these observations may preclude using n-alkanes to measure past treeline movement in these mountains, δD values of biomarkers in fluvial deposits in these settings are more likely to record local hydrological changes rather than reflect fractionation changes due to turnover in the upstream vegetation structure.