AbstractShallow lakes are increasingly recognized as important sites for organic carbon (OC) storage. However, the drivers of OC deposition in shallow floodplain lakes remain unclear due to complex terrestrial and aquatic interactions. Using 8 yr of monthly sediment trap data in a cross‐ecosystem experiment on six UK shallow lakes of varying riverine connectivity, we investigated the role of allochthonous (fluvial materials) vs. autochthonous (phytoplankton production) deposits as the OC supply to lake sediments. Organic carbon sedimentation rates in river‐connected (1.3 ± 1.2 g C m−2 d−1, mean ± SD) and isolated lakes (0.5 ± 0.4 g C m−2 d−1) surpassed those previously published for temperate zone eutrophic lakes. Generalized linear mixed‐effect models identified water column chlorophyll a as the best predictor of OC sedimentation for most lakes, suggesting that autochthonous phytoplankton production was the dominant driver of OC sedimentation, albeit stimulated by riverine nutrient supply. Carbon (C) transfer to the sediments was modulated by flow; during major floods, phytoplankton was likely flushed out of lakes, reducing OC sedimentation. Inorganic carbon sedimentation intermittently contributes substantially to carbon deposition in spring, summer, and winter. This study evidenced that shallow floodplain lakes are important sites for C deposition, with maximum C transfer to the sediments during the growing season. Future increases in hydrological variability could negatively impact the capacity of shallow floodplain lakes to retain and sequester carbon.