Assessing water quality and ecological health of New Zealand’s lakes is challenging, as many are not monitored. For the few lakes that are monitored, datasets are short (<10 years) and were started after lakes had deteriorated. Paleolimnology uses lake sediments as natural archives allowing environmental history to be reconstructed. This data can be used to determine current and historical aquatic communities, and water quality. Environmental DNA (eDNA) analysis has recently been incorporated in paleolimnological studies. This has enabled the characterisation of soft bodied organisms and microbial communities in sediment cores. In this study, we used eDNA to investigate changes, dating back approximately 1,000-years, in bacterial communities of seven lakes with varied historical changes in land-use. We focused on lakes in the Tasman region (New Zealand): two study lakes were situated above the tree line (c. 1,200 m) and surrounded by pristine alpine vegetation; the remaining five were at sea level. Of the latter, one was in a largely unmodified wetland, three had low-intensity agricultural activity (4-30% of their catchment), and the final lake was situated in an urban area. Bacterial communities were analysed by 16S rRNA metabarcoding. There was little change in bacterial community composition in the alpine and wetland lakes. Cyanobacteria and Thermodesulfovibriona increased in the other lakes following European activities in their respective catchment. This study highlights how sediment DNA analyses can complement traditional paleo-approaches and provide novel insights into changes in lake health and provide information on the potential causes.