This study presents trace elements levels in surface and deep sediments of the Toulon bay (SE France) subjected to anthropogenic inputs (navy base, harbors, etc.). The studied elements (As, Cd, Cr, Cu, Hg, Ni, Pb, Zn) are defined as priority contaminants in aquatic systems. Fifty-five points scattered on the entire bay were sampled, allowing the determination of contaminants distribution with a high resolution. Several approaches were used to assess the degree of contamination and the potential toxicity of the Toulon bay sediments: comparison to the French legislation, surface-weighted average metal concentrations, enrichment factors (EF), geoaccumulation indices (Igeo), trace element stock calculation and comparison to sediment quality guidelines. A principal component analysis was performed to reveal common behavior of the studied contaminants. Results demonstrated the very high contamination of the small bay, especially in Hg (EF up to 1500), Cu, Pb and Zn, with export to the large bay further governed by hydrodynamics.