Sediments were grouped in three zones of the bay: two in the northern basin with higher metal contamination; and another in the southern basin, where lithogenic metals were predominant. Sediment pollution classification made using Index of geoaccumulation and Enrichment factor was consistent, indicating higher accumulation of Cd and Pb in the northern basin. The negative influence of activities linked to petrol was predicted by V/Ni and V/(Ni+V) ratios. Cd and Pb did not represent a potential risk; while Cu and Ni could be risky for biota in most sediment, according to Screening Quick Reference Tables (SQuiRTs). Comparison of bioavailable fraction of metals with references in SQuiRTs corroborated the low potential damage on the biota due to As, Cd, Pb, Cr, Zn; and a higher potential damage due to Cu; while an attenuation of the risk due to Ni predicted by SQuiRTs could be expected.