Transitional water ecosystems have low water exchanges and can trap chemicals and microplastics (MPs). In this study, MPs, trace elements, polycyclic aromatic hydrocarbon-PHAs levels and the oxidative stress response were assessed in Mytilus galloprovincialis from two Italian lagoon ecosystems (Orbetello and Varano). In addition, the ecotoxicological effects induced by the exposure of M. galloprovincialis to high-density polyethylene-HDPE MPs were also determined. Levels of trace elements were almost always comparable among the sites, whereas MPs were found only in mussels from Orbetello. PAHs were always under the limit of quantification. Glutathione peroxidase and malondialdehyde levels were significantly higher in mussels from Varano. As regard the exposure test, it was found a significant effect of treatment, site and their interaction on mortality and biochemical biomarkers in both fed and unfed mussels. However, principal component analysis suggests similar effects of both color and nourishment condition on biochemical biomarkers. These findings warrant further investigation.