The increase in global production of carbon nanotubes (CNTs), as well as their use in polymer nanocomposites has raised concerns as to their possible effects on the marine environment that could ultimately affect human populations. Specifically, CNTs have already been tested in antifouling formulations for the prevention of biofouling, mainly to protect ships' hulls, as well as in composite materials that come in contact with seawater. At this point, it seems crucial to assess the possible effects of CNTs on aquatic organisms and assess their toxicity. Thus, in this study, three different model organisms were selected for toxicity testing: Daphnia magna water flea, Artemia salina nauplii and Danio rerio zebrafish. The CNTs that were tested have been produced in house via the chemical vapour deposition method and were fully characterised in order to understand the effect of their properties on the aquatic organisms. In this study pristine multiwalled carbon nanotubes (MWCNTs) as well as functionalised with carboxyl groups were used. Dispersion issues were evident in all tests, both for the pristine and functionalised carbon nanotubes, thus their toxicity could not be determined in relation to their concentration. To overcome this issue, optical observation of the organisms took place. MWCNT black aggregates were clearly observed in the intestine of A. salina. Following an additional 24 h in seawater the intestine appeared clean and restored to its normal appearance. This observation leads to the conclusion that MWCNTs did not prove to be fatal to D. magna and A. salina despite their presence in the digestive track of both non-target organisms. These results show that MWCNTs do not affect the non-target organisms in the short term, thus their use in antifouling coatings and composite materials for maritime applications can be further investigated.