Nanotechnology is a much promising field of science and technology with applications in a wide range of areas such as electronics, biomedical applications, energy and cosmetics. Metal-based engineered nanoparticles (ENPs) are common in many technological applications; some of the most common nanoparticles available commercially are silver, gold, copper oxide (CuO), zinc oxide (ZnO) and cadmium sulphide (CdS). The toxicity of metal-based NPs may be either due to their specific physical characteristics as NPs or to the specific toxicity of metals released from NPs under environmental conditions. In this study we evaluated the toxicity effects of a range of ENPs (Ag, Au, CuO, CdS, ZnO) along with a control containing equivalent quantities of dissolved metal on two endobenthic species: the ragworm Hediste diversicolor and the bivalve Scrobicularia plana. A suite of complementary biomarkers was used to reveal toxicity effects. A common challenge in multibiomarkers studies is to go beyond an independent interpretation of each one, and to assess a global response of individuals. The Integrated Biomarker Response (IBR) was calculated for both species exposed to the different metal-based ENPs studied or to their dissolved metal counterpart to provide efficient and easy tools for environmental managers. We evidence that metal-based NPs lead to an overall difference in biological responses from that of their dissolved counterparts. The IBR could thus be considered as an efficient tool to transfer research results to stakeholders with possible implementation for regulatory purposes.