Despite of the large array of available carbon nanotube (CNT) configurations that allow different industrial and scientific applications of these nanoparticles, their impacts on aquatic organisms, especially on invertebrate species, are still limited. To our knowledge, no information is available on how surface chemistry alteration (functionalization) of CNTs may impact the toxicity of these NPs to bivalve species after a chronic exposure. For this reason, the impacts induced by chronic exposure (28days) to unfunctionalized MWCNTs (Nf-MWCNTs) in comparison with functionalized MWCNTs (f-MWCNTs), were evaluated in R. philippinarum, by measuring alterations induced in clams' oxidative status, neurotoxicity and metabolic capacity. The results obtained revealed that exposure to both MWCNT materials altered energy-related responses, with higher metabolic capacity and lower glycogen, protein and lipid concentrations in clams exposed to these CNTs. Moreover, R. philippinarum exposed to Nf-MWCNTs and f-MWCNTs showed oxidative stress expressed in higher lipid peroxidation and lower ratio between reduced and oxidized glutathione, despite the activation of defense mechanisms (superoxide-dismutase, glutathione peroxidase and glutathione S-transferases) in exposed clams. Additionally, neurotoxicity was observed by inhibition of Cholinesterases activity in organisms exposed to both MWCNTs.