Environmental archives, such as lake sediments, harbour DNA of past and present ecosystems. However, our understanding of the provenance, deposition and distribution of sedimentary DNA in lake systems is largely unknown, limiting the breadth of derived spatiotemporal inferences. By mapping the distribution of aquatic and terrestrial taxa in a large deep lake using metabarcoding, we characterise the spatial heterogeneity of sedimentary DNA and point to its potential driving factors. Taxa composition varies across geographic gradients in the lake, and spatial distribution of DNA is linked to the range and life mode of organisms. Exogenous taxa, such as alpine plants, have the most reliable detection near the mouth of the inflow. Our data reveal that sedimentary DNA is reflecting the mosaic distribution of organisms and organic remains in the environment, and a single location from lakes with watersheds across different elevations, biomes or other diversity boundaries does not capture the full dynamics in the surrounding area.