The potential for ecological toxicity associated with nanomaterials is a growing area of investigation, in particular in the aquatic environment. In suspension feeding invertebrates, the cellular immune system and digestive gland are likely to be targeted, due to their highly developed processes for the cellular internalisation of nano- and micro-scale particles that are integral to key physiological functions such as cellular immunity and intracellular digestion. We have recently demonstrated that suspensions of selected commercial nanomaterials, namely Nano carbon black (NCB), C60 fullerene (C60), Nano-titanium dioxide (n-TiO2) and Nanosilica (n-SiO2) induce oxyradical production and lysosomal enzyme release in the hemocytes of the marine mussel Mytilus in vitro. In this work the possible effects of in vivo exposure to these NPs were investigated. Mussels were exposed to different concentrations (0.05-0.2-1-5mg/l) of NP suspensions for 24h and different biomarkers were evaluated in hemocytes, digestive gland and gills. Characterisation of NP suspensions in artificial sea water (ASW) was performed, indicating the formation of agglomerates of different sizes in the nano-micromolar range for different types of NPs. Formation of larger agglomerates was observed at the end of exposure. The results show that all NP suspensions induced significant lysosomal membrane destabilisation in both the hemocytes and the digestive gland, with NCB>>C60>n-TiO2, >n-SiO2. In the digestive gland, all NPs induced lysosomal lipofuscin accumulation only at the highest concentrations tested to a different extent depending on the NP type. NCB, TiO2 and SiO2 also induced lysosomal neutral lipid accumulation. Moreover, all NPs increased the activity of the antioxidant enzyme catalase, with n-SiO2>NCB≅TiO2>C60; NCB and n-TiO2 also stimulated glutathione transferase (GST). Changes in catalase and GST activities were also observed in gills, with both increases and decreases depending on NP type and concentration. The reported results demonstrate that in mussels responses to exposure to NP suspensions involve changes in lysosomal and oxidative stress biomarkers in the digestive gland, suggesting uptake of NP aggregates/agglomerates mainly through the digestive system. Overall, these data further support the hypothesis that suspension feeding invertebrates represent a significant target for NPs in the aquatic environment.