A long-standing enigma in oceanography is why terrestrial organic matter is "missing" in the global ocean, despite the considerable discharge into it every year. Although some explanations, such as mineralogical composition, hydrodynamic processes, and priming effect, have been proposed, we hypothesize that the essential mechanism behind the missing organic matter is microbial processing, for which the underlying coupled geochemical, molecular, and genetic evidence is unknown. An ultra-large-volume, long-term river-seawater stratified simulation system was constructed to unravel the microbially driven fate of terrigenous particulate organic matter (POM) in oceans. Analysis of combining the molecular with POM chemical composition data suggests that Bacteroidetes could act as pioneers in the processing of terrigenous POM in oceans, degrading high-molecular-weight, high-carbon compounds such as polysaccharides. Remaining low-molecular-weight nitrogenous organic matter is subsequently degraded by Planctomycetes and Proteobacteria. Isotopic signals show that this preferential degradation causes a distinct "aging" effect of POM, and along with nitrification enhanced by remineralization, causes a decrease in the POM C : N ratio. Degradation of terrigenous POM and bacterial biomass biosynthesis leads to positive deviations in δ 15 N and δ 13 C. Relatively refractory hydrocarbons, aromatic compounds, and phenols are accumulated by microbial processes in this system. This study provides mechanistic insights into the missing chemical and isotopic signals and microbially driven fate of terrigenous POM in the ocean, with important implications for how riverine material input affects marine carbon and nitrogen cycling.Ongoing climate change is expected to lead to increased global river runoff (Labat et al. 2004;Andersson et al. 2015). Both ecological modeling and field research have indicated that the flux of terrestrial input to oceans increases with increased river runoff (Andersson et al. 2015). However, few molecular signals of abundant terrestrial organic matter are detected in marine environments (Hedges et al. 1997;Bianchi 2011;Kandasamy and Nath 2016), and only a trace of terrigenous organic matter (e.g., lignin) is present in the ocean (Opsahl and Benner 1997). A proposed explanation for this is a priming effect, in which the addition of labile organic carbon increases remineralization of the relatively refractory organic carbon (Bianchi 2011;Morling et al. 2017). Mineralogical composition and characteristics have also been proposed as important factors controlling the fate of continentally