Eutrophic shallow lakes are hotspots of carbon (C) and nitrogen (N) accumulation and transformation, and are increasingly recognized as important sources of greenhouse gases (GHGs: CO2, CH4 and N2O). Lacustrine groundwater discharge (LGD) is a crucial component of the water budget and terrestrial material delivery for lakes, but its interplays with intrinsic CN biogeochemical processes remain less tackled. In this study, C and N ingredients and multiple stable isotopes (δ2H, δ18O, δ13C, and δ15N) were measured seasonally in groundwater, river water and lake water of a large eutrophic shallow lake in eastern China. The results revealed that groundwater is enriched with various forms of C and N that have similar sources and pathways as surface water in the lake and rivers. The isotope balance model also indicated that LGD derived C and N contribute significantly to lake inventories in addition to river runoff. These allochthonous C and N provide extra substrates for related biogeochemical processes, such as algae proliferation, organic matter degradation, methanogenesis and denitrification. Simultaneously, the excess oxygen consumption leads to depletion and hypoxia in the lake, further facilitating the processes of methanogenesis and denitrification. LGD functions not only as an external source of C and N that directly increases GHG saturations, but also as a mediator of internal CN pathways, which significantly affect hypoxia formation, GHG productions and emissions in the eutrophic lake. This study highlights the unrevealed potential regulation of LGD on biogeochemical processes in the eutrophic lake, and underscores the need for its consideration in environmental and ecological studies of lakes both regionally and globally.