A study to determine total and mobile heavy metals concentrations in sediments from Algeciras Bay was performed and pollution hotspots were identified. The effects on aquatic organisms were established using sediment quality guidelines (SQGs). Ni and Cr exceeded the effect range medium and low levels, respectively, around industrial area. Potential toxicity of metals was determined by diethylenetriaminepenta-acetic acid (DTPA) extractions and low alert levels of Co. Cu, Zn, Cd. Ni and Pb were exceeded at most sampling sites. Three pollution indicators were used showing significant values for As, Ni, Cr, Pb and Cd. Sediment speciation using the sequential extraction BCR procedure was carried out, being Cd, Zn, Pb and As the most available metals. Principal component, cluster and ANOVA analyses were performed in order to assess the sources of metals and the influence of seasonality and anthropogenic activities on the sediment quality. Two principal component analysis (PCA) factors were obtained identifying the sampling sites affected by anthropogenic activities; Ni-Cr and Zn-Cu-V clusters were also obtained associated with stainless steel and petrochemical industrial activities. ANOVA showed the outstanding sites because of total metal concentration and significant differences among sampling sites by the acid extractable and reducible fractions for all metals except for Ba and V. (C) 2011 Elsevier B.V. All rights reserved.