Retrieval of modern and ancient environmental DNA (eDNA) from sediments has revolutionized our ability to study past and present ecosystems. Little emphasis has been placed, however, on the fundamentals of the DNA–sediment associations in environmental settings. Consequently, our understanding of mineralogic controls and geochemical processes that take place on the DNA–sediment interface, and its implications for eDNA taphonomy and provenance, remain extremely limited. Here, we apply interfacial geochemical principles to elucidate how depositional processes and the stability of DNA–sediment associations in different environments can influence our interpretation and identify possible interpretational biases arising from neglecting mineral and geochemical controls on eDNA taphonomy. We use atomic force microscopy to show how interfacial geochemical interactions drive DNA adsorption behavior and we outline how to increase the scope and resolution of ecological interpretations from eDNA by combining mineralogic composition information with experimental adsorption data. We bring the concepts together and propose how to integrate sediment provenance as well as mineralogic and geochemical principles in eDNA taphonomy analysis for improved reconstruction of past ecosystems and monitoring of modern ecosystems from eDNA data. We provide a conceptual understanding of how eDNA taphonomy and sediment provenance can be addressed and further applied to enhance the scope, resolution, and accuracy of modern and past ecological reconstructions based on eDNA data.