Ecosystems are under the pressure of complex mixtures of contaminants whose effects are not always simple to assess. Biomarkers, acting as early warning signals of the presence of potentially toxic xenobiotics, are useful tools for assessing either exposure to, or the effects of these compounds providing information about the toxicant bioavailability. In fact, it has been argued that a full understanding of ecotoxicological processes must consider an integrated multi-level approach, in which molecular impact is related with higher-order biological consequences at the individual, population and community levels. Monitoring programs should make use of this tool to link contaminants and ecological responses fulfilling strategies like those launched by OSPAR (Commissions of Oslo and Paris) Convention on the protection of the marine environment of the North-East Atlantic and the International Council for the Exploration of the Sea (ICES). An overview of the work done in the past few years using biomarkers as in situ tools for pollution assessment in Portuguese coastal waters is presented as a contribution to the set up of a biomonitoring program for the Portuguese coastal zone. Considering the data set available the biomonitoring proposal should include the analysis of biomarkers and effects at individual levels. The aim of the program will include a spatial and temporal characterization of the biomarkers acetyl-cholinesterase, metallothioneins, DNA damage, adenylate energy charge and scope-for-growth levels. The investigation of the spatial variation of biomarkers is crucial to define sites for long term monitoring, which will be integrated with a chemical monitoring program. This framework will be a major contribution to the implementation of a national database for the use of biomarkers along the Portuguese coast.