This study refers to the integrative assessment of sediment quality in three harbour areas at the Spanish Atlantic Coast: Vigo (Northwestern Spain), Bilbao and Pasajes (Northern Spain). At each site, two lines of evidence have been considered: chemical analyses (metal, PAH and PCB concentrations in sediments and ammonia concentration in bioassays) and toxicity tests (Microtox®, Corophium sp. marine amphipod and Paracentrotus lividus sea urchin larvae). Chemical and ecotoxicological results have been integrated by means of a tabular matrix and a multivariate factorial analysis (FA). Highly toxic samples have been characterised in Vigo and Pasajes harbours while Bilbao samples present toxicity levels ranging from non-toxic to moderately toxic. High toxicity is associated with high levels of contaminants whereas confounding factors (ammonia, organic matter and mud) have been identified to be the main cause of low to moderate toxicity. Based on the obtained results, it can be concluded that deriving potential toxicity of sediments based on comparison with Sediment Quality Guidelines (SQGs) is in agreement to toxicity results in areas presenting high levels of contaminants. However, at lower levels of toxicity (low to moderate), the mismatch between the potential toxicity (SQG approach) and the toxicity measured by bioassays is greater, as the former only accounts for chemical concentrations, without considering the interaction between contaminants and the effect of confounding factors. Contrarily, the multivariate analysis seems to be a robust tool for the integration and interpretation of different lines of evidence in areas affected by different sources of contamination.