Inventories of organisms are central to ecological research and to ecosystem management. Environmental DNA (eDNA) methods permit broad yet detailed biodiversity sampling to be performed with minimal field effort, but uncertainty remains regarding the spatial resolution necessary for effective sampling. We analyze eDNA samples from twelve temperate lakes via ITS1 rRDNA metabarcoding for aquatic and terrestrial plant taxonomic patterns across horizontal and vertical space. We detect the expected community variation (beta diversity) from lake to lake, but few community composition patterns related to offshore distance and sampling depth. Patterns included slightly elevated alpha diversity in near-shore samples, but no other significant effects. Read abundances were heavily weighted toward aquatic macrophytes, but we identified representatives of many other phylogenetically and environmentally varied taxa, including terrestrial species from surrounding areas. We conclude that freshwater plant eDNA surveys successfully capture differences among lake communities, allowing easily-accessible shore-based sampling to inform research and management.