During the last decade, compound-specific hydrogen isotope analysis of plant leaf-wax and sedimentary n-alkyl lipids has become a promising tool for paleohydrological reconstructions. However, with the exception of several previous studies, there is a lack of knowledge regarding possible effects of early diagenesis on the dD values of n-alkanes. We therefore investigated the n-alkane patterns and dD values of long-chain n-alkanes from three different C3 higher plant species (Acer pseudoplatanus L., Fagus sylvatica L. and Sorbus aucuparia L.) that have been degraded in a field leaf litterbag experiment for 27 months. We found that after an initial increase of long-chain n-alkane masses (up to not, vert, similar50%), decomposition took place with mean turnover times of 11.7 months. Intermittently, the masses of mid-chain n-alkanes increased significantly during periods of highest total mass losses. Furthermore, initially high odd-over-even predominances (OEP) declined and long-chain n-alkane ratios like n-C31/C27 and n-C31/C29 started to converge to the value of 1. While bulk leaf litter became systematically D-enriched especially during summer seasons (by not, vert, similar8‰ on average over 27 months), the dD values of long-chain n-alkanes reveal no systematic overall shifts, but seasonal variations of up to 25‰ (Fagus, n-C27, average not, vert, similar13‰). Although a partly contribution by leaf-wax n-alkanes by throughfall cannot be excluded, these findings suggest that a microbial n-alkane pool sensitive to seasonal variations of soil water dD rapidly builds up. We propose a conceptual model based on an isotope mass balance calculation that accounts for the decomposition of plant-derived n-alkanes and the build-up of microbial n-alkanes. Model results are in good agreement with measured n-alkane dD results. Since microbial ‘contamination’ is not necessarily discernible from n-alkane concentration patterns alone, care may have to be taken not to over-interpret dD values of sedimentary n-alkanes. Furthermore, since leaf-water is generally D-enriched compared to soil and lake waters, soil and water microbial n-alkane pools may help explain why soil and sediment n-alkanes are D-depleted compared to leaves.