Biofouling is one of the most challenging problems for the maritime industry which has been minimized through the application of coatings containing anti-fouling (AF) biocides (e.g. Cu-based compounds; DCOIT) in immersed structures. An innovative eco-friendly approach based on the encapsulation of AF biocides in engineered nanomaterials (e.g. mesoporous silica nanocapsules (SiNCs)) has recently been applied to control the leaching rate and the environmental impacts of AF biocides when used as additives in coatings. Thus, the present study aims to: (a) assess the toxicity towards marine species of three innovative AF nanomaterials: SiNCs loaded with DCOIT (SiNC-DCOIT), SiNCs coated with silver (SiNC-Ag), SiNCs loaded with DCOIT and coated with silver (SiNC-DCOIT-Ag), and free counterparts (DCOIT, ionic silver and empty SiNCs) and (b) test if encapsulation reduces the toxicity of biocides to non-target species maintaining the anti-fouling efficacy against target species. To achieve this goal, eleven marine species (three target and eight non-target) were exposed to the test compounds, following standard protocols, with adaptations for some species. DCOIT and silver were found to be very to extremely toxic to the target and non-target species tested. Encapsulated biocides reduced their toxicity towards non-target species while showing good AF performance towards fouler species. The present study demonstrated that the encapsulation of DCOIT and silver in silica nanocapsules is a promising, efficient and more environmentally-friendly anti-fouling solution compared to free commercial biocides.