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There has been a worldwide increase in the number of Marine Protected Areas and marine reserves over the last decade. In these areas, the protection measures adopted are related to specific management goals; nevertheless, actual knowledge of the effectiveness of the restrictions is far from exhaustive. This article aims to contribute to knowledge of the environmental quality of the marine reserves in the Tuscan Archipelago (Mediterranean central area) which is composed of seven islands at different levels of protection. A monitoring programme spanning multiple years was performed on water and sediment samples to finalise a definition of the trophic levels and the response of microbiological indicators (total heterotrophic bacteria, Actynomyces, hydrocarbon-degrading bacteria) to persistent organic pollutants (polychlorinated biphenyls, 1,1-bis-(4-chlorophenyl)-2,2-dichloroethene, hexachlorobenzene and polybrominated diphenyl ethers) was assessed. The results showed that these reserves were generally of good quality. A clear fingerprint produced by human activities along the coast and significant differences relating to the level of protection were observed. There exists the need to also consider basin dynamics when planning the protection management strategies adopted for marine reserves. [ABSTRACT FROM AUTHOR]