Studies have described the occurrence of nanoparticles (NPs) in aquatic ecosystems, with particular attention to the widely commercialized carbon nanotubes (CNTs). Their presence in the environment raises concerns, especially regarding their toxicity when co-occurring with other pollutants such as metals. In the present study, changes to the metabolic capacity, oxidative, and neurologic status were evaluated in the presence of carboxylated multi-walled CNTs and chromium (Cr(III)) using two of the most ecologically and economically relevant filter feeder organisms: the clam species Ruditapes decussatus and R. philippinarum. Results indicated that although Cr, either alone or in combination with CNTs, was found in a similar concentration level in both species, a species-specific Cr accumulation was observed, with higher values in R. decussatus in comparison with R. philippinarum. Inhibition of antioxidant defenses and neurotoxic effects were detected only in R. philippinarum. The interaction between contaminants seems to have no effect in terms of antioxidant enzyme activities and neuro status. Nevertheless, synergistic activation of responses to both contaminants may have altered the metabolic capacity of bivalves, particularly evident in R. decussatus. While both clams are tolerant to both contaminants (alone and together), they showed a relevant accumulation capacity, which may represent a possible contaminant transfer to humans.