Environmental archives, such as lake sediments, harbor DNA evidence from past and present ecosystems. However, our understanding of the provenance, taphonomy and distribution of sedimentary DNA in lake systems is largely unknown, limiting the breadth of spatiotemporal inferences drawn from it. To address this gap, we studied surface sediments across Lake Constance using DNA metabarcoding, and mapped the distribution of sedimentary DNA targeting diverse organismal groups: plants, eukaryotes, cyanobacteria, and copepods. We find dissimilarity across all sites to increase with distance and the spatial distribution of DNA to vary among different groups of taxa and life modes. Our data reveal that DNA from a single sediment core from lakes with watersheds across different elevations, biomes or other diversity boundaries does not capture the full dynamics of the surrounding area but is reliable for widely distributed taxa. At larger spatial surveying scales, sedimentary DNA possesses the potential for efficient high-resolution biodiversity mapping.