Information on nanomaterial interactions with co-contaminants, including their influence on toxicity and environment fate in aquatic environment is rather limited. In this study, the effect of multiwall carbon nanotubes (MWCNTs) co-exposure on the toxicity, biodegradation and bioaccumulation of carbamazepine (CAB) in diatom Navicula sp. was evaluated. Results showed that the three tested MWCNTs showed high sorption capability of CAB, especially for hydroxyl-functionalized MWCNT (OH-MWCNT) with a Q of 24 and 0.7 times higher than that of two pristine MWCNTs (pMWCNT-1 and pMWCNT-2), respectively. The pMWCNT-1 posed no significant effects on growth of Navicula sp., whereas the algal growth was inhibited by 10 mg L pMWCNT-2 (P < 0.05). The toxicity of pristine MWCNTs to algae increased with the diameters. OH-MWCNT stimulated the growth of Navicula sp. within 72 h, indicating that surface functionality of MWCNTs played a role in toxicity to Navicula sp. The presence of pMWCNT-1 and pMWCNT-2 could significantly aggravate the toxicity of CAB to Navicula sp., while OH-MWCNT exhibited insignificant effect on CAB toxicity. MWCNTs with a concentration of <10 mg L played a protective role in the photosynthetic function of Navicula sp. Both pMWCNT-1 and pMWCNT-2 had no significant effect on the removal of CAB by Navicula sp., but OH-MWCNT could inhibit the degradation of CAB at the end. MWCNT co-exposure suppressed the bioavailability of CAB in Navicula sp. The results from the present study clearly demonstrated that CAB could be sorbed onto the surface of MWCNTs and sorption of CAB on MWCNTs had a key effect on the toxicity, biodegradation and bioaccumulation of CAB. The physicochemical properties and surface functionality of MWNCTs played an important role in toxicity and fate of CAB to Navicula sp.