Lithium isotopes are a promising proxy for reconstructing past weathering processes, but unraveling the seawater record requires a comprehensive understanding of the magnitude and isotopic composition of Li fluxes to the oceans, and of how these change over time. Little information is available on the role of floodplain sediments and groundwater systems in setting the Li isotope signature of the dissolved flux delivered from the continents to the oceans. Here we investigate the Li dissolved fluxes of river waters and groundwaters in the Ganges–Brahmaputra floodplain. The data suggest that a maximum of 3.1×108 and 1.5×108 moles Li/yr are carried to the Bay of Bengal by Ganges–Brahmaputra rivers and groundwaters, respectively. The riverine flux has a significantly heavier Li isotope composition (average δ7Li: 26‰) than the groundwater flux (average δ7Li: 16‰) and increases downstream across the floodplain. δ7Li in both river waters and shallow groundwater can be explained by Li scavenging by Quaternary floodplain sediments following a Rayleigh fractionation process, with preferential removal of 6Li. On the other hand, deep groundwaters (>40 m) contributing to submarine groundwater discharge to the Bay of Bengal are enriched in 6Li at depth, likely due to the dissolution of floodplain sediments releasing Li with a light isotope composition. Similarly low δ7Li has been reported in other large sedimentary aquifers. The deep groundwater values are close to the average isotope composition of the global Li inputs to the ocean (∼15‰), so groundwater submarine discharge has only a minor influence on the assessment of the modern Li isotope budget of the ocean. Our analysis further suggests that groundwater discharge of Li has probably played at most a small and secondary role in past changes in the isotope composition of the total continental flux of Li to the ocean.