This study investigated the effect of carbon nanotubes (CNTs) and titanium dioxide (TiO2) incorporated in PDMS on biofilm formation and plantigrade settlement of Mytilus coruscus. TiO2 increased bacterial density, and CNTs also increased bacterial density but reduced diatom density in biofilms after 28 days. Further analysis was conducted between bacterial communities on glass, PDMS, CNTs (0.5 wt%) and TiO2 (7.5 wt%). ANOSIM analysis revealed significant differences (R > 0.9) between seven, 14, 21 and 28 day-old bacterial communities. MiSeq sequencing showed that CNTs and TiO2 impacted the composition of 28 day-old bacterial communities by increasing the abundance of Proteobacteria and decreasing the abundance of Bacteroidetes. The maximum decreased settlement rate in 28 day-old biofilms on CNTs and TiO2 was > 50% in comparison to those on glass and PDMS. Thus, CNTs and TiO2 incorporated in PDMS altered the biomass and community composition of biofilms, and subsequently decreased mussel settlement.