Sediments are complex heterogeneous matrices allowing to some extent the recording of past environmental conditions by integrating sediment characteristics, contamination and the microbial community assembly. In aquatic environments, abiotic environmental filtering is considered the primary deterministic mechanism shaping microbial communities in sediments. However, the number and relative contributions of geochemical and physical factors associated with biotic parameters (reservoir of microorganisms) complicate our understanding of community assembly dynamics. In this study, the sampling of a sedimentary archive in a site alternately subjected to contrasting inputs from the Eure and the Seine Rivers allowed us to study the response of microbial communities to changes in depositional environment over time. The coupling of the quantification and sequencing of the gene encoding the 16S rRNA with analyses of grain size, organic matter and major and trace metal contents demonstrated that microbial communities reflected contrasting sedimentary inputs over time. Total organic carbon (TOC) was the main factor influencing microbial biomass, while the quantity and quality of organic matter (R400, RC/TOC), major elements (i.e. Al, Fe, Ti) and trace metals (i.e. Zn, Pb, Cu, Cr, Ni, As, Co, Ag, Sb) shaped the structure of the microbial community. Besides the effect of geochemical factors, a specific microbial signature was associated with the contrasting sedimentary sources, highlighting the importance of the microbial reservoir in the assembly of microbial communities. Indeed, the main genera identified in the facies influenced by the Eure River were affiliated with the phyla Desulfobacterota (Syntrophus, Syntrophorhabdus, Smithella, Desulfatiglans), Firmicutes (Clostridium_sensu_stricto_1), Proteobacteria (Crenothrix), Verrucomicrobiota (Luteolibacter), while the contributions of the Seine River were characterised by some halophilic genera Salirhabdus (Firmicutes), Haliangium (Myxococcota) SCGC-AB-539-J10 (Chloroflexi). This study sheds light on the overall processes determining the assembly of microbial communities in sediments and the importance of associating geochemical factors with reservoirs of microorganisms inherited from sediment sources.