Display omitted •This is the first study on metals pollution in this Mediterranean Bay.•Environmental quality guidelines were used to assess the potential ecological risks.•The fractionation analysis of sediments showed the bioavailability of the metals.•Statistical analyses aided to better understanding of pollution sources.•Statistical analyses aided to localize the areas more polluted. Concentrations of heavy metals were measured in sediment and water from Málaga Bay (South Spain). In the later twentieth century, cities such as Málaga, have suffered the impact of mass summer tourism. The ancient industrial activities, and the actual urbanization and coastal development, recreation and tourism, wastewaters treatment facilities, have been sources of marine pollution. In sediments, Ni was the most disturbing metal because Ni concentrations exceeded the effects range low (ERL), concentration at which toxicity could start to be observed in 85% of the samples analyzed. The metal bioavailability decreased in the order: Cd>Ni>Pb>Cu>Cr. In the sea water samples, Cd and Pb were the most disturbing metals because they exceeded the continuous criteria concentration (CCC) of US EPA in a 22.5% and 10.0% of the samples, respectively. Statistical analyses (ANOVA, PCA, CA) were performed.