In the context of growing anthropogenic disturbances that deeply alter marine coastal ecosystems, various management tools are used to protect biodiversity, such as fishing gear limitations, fishing quotas, protected areas or the creation of artificial reefs (ARs). In contrast to the other management tools, ARs require a modification of natural habitats. We used underwater visual censuses to investigate the effect of habitat modification on the structure of fish communities by comparing a natural reef (NR) to ARs with different habitat complexity. Different fish assemblage descriptors were used to assess species- and functional- and community-level aspects of the assemblages. ARs were rapidly colonized by adult fishes and presented community compositions different from that of the NR. Fish densities and functional richness were higher in the ARs than in the NR. Small isolated artificial structures, such as culverts and box-culverts, had different fish community compositions than more extended and complex structures, demonstrating the effect of structural habitat complexity on fish assemblages. Fish density was higher in small structures, most likely due to habitat isolation and patchiness. This study indicates that ARs which are located along sandy coastal areas with few rocky habitats and under high river nutrient influence are a suitable habitat for rocky coastal fish communities. Nevertheless, due to higher habitat complexity and lower fishing pressure on ARs, fish communities of an AR functionally differ from those of a NR. Further research is necessary to understand how these differences act on the properties of the ecosystem as well as on local fisheries