Ancient environmental DNA (eDNA) preserved in disseminated materials (e.g. sediments, soils, ice, and palaeofaeces) has been shown to be a viable target for reconstructing a wide taxonomic breadth of ancient ecosystems in diverse depositional contexts. This is most remarkably true even in the total absence of surviving primary tissues from those organisms. Canadian archaeological sites are, on average, well suited to analyses of this kind with low mean annual temperatures facilitating ancient DNA preservation—being contingent, of course, on microclimatic conditions in the burial environment such as water/oxygen content, pH, and microbial communities. Ecologists are increasingly utilizing eDNA to monitor shifting contemporary ecosystems to mitigate the need for logistically burdensome ground surveys. For archaeologists, the systematic collection of environmental samples from sites at risk or from those being excavated has the potential to substantially increase our taxonomic resolution of ancient human ecosystems. However, these ancient biomolecules are not themselves impervious to degradation from shifting environments. Permafrost is particularly vulnerable in the Canadian north not only from thaw slump placing infrastructure and heritage sites at risk, but also for degrading the Quaternary molecular archives of exceptionally well-preserved ancient DNA therein. Here, I discuss how the collection of environmental samples for future analyses with ancient DNA techniques may help mitigate some degree of the information loss expected from ‘heritage at risk’ sites. As well as discussing a forthcoming lake sediment investigation as an example of the increasing analytic power of sedimentary ancient DNA methods.