In a time of unprecedented global environmental change, understanding the response of biodiversity is paramount. However, our knowledge of anthropogenic impacts on ecosystems is limited by a lack of standardized retrospective biomonitoring data. Here, we use four-decade time series of archived blue mussels to trace spatiotemporal biodiversity change in coastal ecosystems. The filter-feeding mussels can serve as natural eDNA samplers, carrying an imprint of the surrounding aquatic community at the time of sampling. By sequencing the preserved DNA, we characterize highly diverse mussel-associated communities and reconstruct the invasion trajectory of an invasive species to the detriment of native taxa uncovering repeated population collapses and reinvasions after cold winters. Time series of natural eDNA samplers provide highly resolved temporal data on community assembly and global warming-driven invasion processes and overcome critical shortfalls in our understanding of biodiversity change in the Anthropocene.