Human activities and climate change have significant impacts on the functioning of coastal ecosystems. Analyzing the dynamics of microbial communities and species offers valuable insights into these changes. Environmental genomics, particularly the use of environmental DNA (eDNA) to assess microbial biodiversity in water or sediment samples, has opened new avenues for evaluating these impacts. These approaches now enable the development of innovative tools for environmental monitoring and management through the study of coastal microbiomes. River inputs and the materials they transport contribute to variability in the composition of micro-eukaryotic communities in estuarine sediments (ECOMINE project). These inputs create gradients in community composition (ROME) and drive potential interactions among microorganisms (ROME/BIOcean5D). Such variations help identify bacterial bioindicators of anthropogenic pressures, which can be applied across Europe to assess freshwater inputs, even in offshore marine ecosystems (OBAMA-Next project). At the same time, new monitoring systems are being developed to detect health, environmental, and marine biodiversity risks (ROME, Ostreobila, BIOcean5D). Ancient sedimentary eDNA analysis allows us to assess ecosystem states prior to significant human influence, across centuries and throughout the Anthropocene. This approach reveals irreversible shifts in species and community structures (PALMIRA), as well as biodiversity losses linked to pollution or intensive industrial activities like mining (HISTOMINE). The link between biodiversity and human-induced pollution is currently being studied at the European scale. Using paleogenetic techniques, researchers aim to identify the effects of eutrophication, urbanization, industrialization, aquaculture, and coastal artificialization. These studies also examine ecosystem resilience (BIOcean5D, TREC, PaleoBreizh) and assess the impact of ecological restoration and biodiversity conservation efforts in marine protected areas (SeaMap). Ultimately, this research aims to define microbial bioindicators of pollution across Europe (TREC, CONTRAST), with potential applications for the sustainable management and conservation of coastal ecosystems.