Natural metal background levels in sediments are critical to assess spatial and temporal trends of contamination in hydrosystems and to manage polluted sediments. This is even more sensitive that multi-factors such as geogenic basement, depositional context, and past or long-term pollution can affect the level of metals in sediments. This article provides natural metal background levels and ancillary data (location, chronology, grain-size, total organic carbon – TOC) in pre-industrial sediments along the Rhône River (France). Two distinct areas were selected to take into account the geological variability of the watershed: the Dauphiné Lowlands (Upper Rhône River) and the Tricastin Floodplain (Middle Rhône River). On each area, the sediment cores were retrieved from palaeochannel sequences and the sampled sections were dated by radiocarbon from the Roman to the Modern Times (AD 3–1878). Regulatory metals (Al, Fe, Cd, Cr, Cu, Ni, Pb, and Zn) and other trace elements (Ba, Co, Li, Mg, Mn, Na, P, Sr, Ti, V) were analysed following both Aqua Regia (AR) and Total Extraction (TE) procedures. Classically, TE provides metal concentrations greater than AR because TE includes crystalline lattice, while AR is close to the potentially bio-accessible part of metals (used for ecotoxicological purposes). Due to the small number of samples and to the non-normal distribution of the results, a median-based approach was chosen to establish the geochemical background values and ranges (MGB) for each sample and area. These MGBs are valuable to identify pollution sources, to characterise a contamination (spread and timing), and to estimate the state of rivers regarding pollution legacy. Along the Rhône River, these two continental MGBs were used to reconstruct the metal geo-accumulation trajectories in river sediments from 1965 to 2018 [1].