During the last decade, an increasing number of studies were interested in the use of lake sediment DNA to trace past landscape changes (plant DNA), agricultural activities (plant, mammal and bacteria DNA) as well as the human presence (human-specific bacteria DNA). However, as all sedimentologists know, the sedimentation in a lake can vary temporally and spatially depending of the variations of processes at the origin of the sediment formation. Moreover, depending on the geological, topographical, climatic and ecological contexts, the sedimentation can be very different from a lake to another. These lake sediments characteristics might affect the aDNA archiving in a various ways including potential biases related to both, the taphonomic processes (DNA source, transfer and deposit) and the analytical process. Consequently, it is now crucial to study these processes to ensure reliable interpretations of the lake sediment DNA results and to improve its potential for palaeoenvironmentalists, archaeologists and historians. In this aim, we combined sedimentological/geochemical analyses with DNA metabarcoding analyses (focused on plants and mammals) on three different mountain lake-catchment systems in the Alps (different relative to their physico-chemical and biological characteristics). We showed the extracellular aDNA retrieved from the sediment mainly comes from upper soil horizons and is transported to the lake being fixed into/onto soil particles. Lakes with high detrital inputs are thus more suitable to archive terrestrial DNA than lakes dominated by autochthonous sedimentation. Furthermore, the hydrographical web has to be well developed to provide a good spatial representativeness of possible plant patches in the catchment. Specific chemical/biological conditions affecting aDNA preservation and/or analysis success were also proposed as explanation for the non-detection of aDNA in one of the lakes. Other less predictable factors, e.g. pastoral practices and animal behaviour, also affect the archiving of aDNA from domestic animals. In particular, determining the type of source of DNA (“point” vs “diffuse”), these factors will affect the detection probability of the animals. All the factors affecting the aDNA record in lake sediments can change over time and can thus significantly affect the reconstructions of plant cover and livestock farming/pasturing histories.