Sea surface temperatures (SSTs) and land-derived input time series were generated from the Gulf of Lions inner-shelf sediments (NW Mediterranean Sea) using alkenones and high-molecular-weight odd-carbon numbered n-alkanes (TERR-alkanes), respectively. The SST record depicts three main phases: a warm Early Holocene ( ∼  18 ± 0.4  °C) followed by a cooling of  ∼  3  °C between 7000 and 1000 BP, and rapid warming from  ∼  1850 AD onwards. Several superimposed multi-decadal to centennial-scale cold events of  ∼  1  °C amplitude were also identified. TERR-alkanes were quantified in the same sedimentary horizons to identify periods of high Rhone River discharge and compare them with regional flood reconstructions. Concentrations show a broad increase from the Early Holocene towards the present with a pronounced minimum around 2500 BP and large fluctuations during the Late Holocene. Comparison with Holocene flood activity reconstructions across the Alps region suggests that sediments of the inner shelf originate mainly from the Upper Rhone River catchment basin and that they are primarily delivered during positive North Atlantic Oscillation (NAO).