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Evaluating the ecological impact of an oil spill is a complex issue requiring coherently articulated examination of the sequence of interactions that link the cell, where contaminants exert their effects, to the ecosystem, where interactions with human activities arise. This sequence of interactions traverses the frontiers between scientific disciplines (chemistry, toxicology, physiology, and fisheries ecology). Using the common sole (Solea solea L.) as a model species for the coastal habitats polluted by the “Erika” oil spill, our research project attempted to define indices of functional integrity that characterised the consequences of fuel exposure at the different biological levels. The coupling of field observations with experimental laboratory work revealed how functional alterations which are readily observable within individuals and their organs are progressively obscured as investigation progresses towards more complex organisational levels. Some of the approaches and indices are proposed as instruments for evaluating the impact of contamination by hydrocarbons.