Estuaries can be considered as biogeochemical reactors, acting both as sinks or sources for trace metals depending on environmental factors. Distribution of dissolved and particulate Cd, Co, Cu, Mn, Ni, and Zn were determined in samples collected from the Loire river estuary (France) during seasonal contrasting flow conditions (summer, spring and winter). Mean concentrations of dissolved Cd (0.13 ± 0.07 nM) were below concentrations previously observed in the estuary, while Cu (23.00 ± 8.07 nM) concentrations were similar to those found ten years ago. The results also demonstrated a wide fluctuation of the TMZ (Turbidity Maximum Zone) following the water discharge conditions and various reactivity behaviours depending on the type of metal even if all metals presented stable log KD values along the estuary. Rapid adsorption of suspended matter occurs at the salinity front, and only Ni and Cu are conservative through the salinity gradient. Organic matter appeared to be a major factor in metals fractioning and its role though the estuary is discussed. Riverine particulate and dissolved metal inputs, and estuary dissolved efflux have been estimated, and show a large export of Cu and Zn to the sea. However, the Loire river outputs only play a minor contribution to the ocean at the global scale. These results provide unique information concerning the contemporary distribution of dissolved and particulate trace metals in the Loire estuary, and provide a geochemical baseline dataset to assess the evolution of historical contaminants in the estuary. Ongoing studies on emerging metallic elements must be carried out to understand the impact of urban development in this part of the river.