Artificial coastal structures, such as seawalls, breakwaters, and groins, can exert various impacts on the fish communities in the nearby regions. This study focuses on assessing the ecological effects of coastal infrastructure on marine environments, by comparing, at different seasons, the habitat complexity and heterogeneity, as well as their effects on fish assemblages, between the artificial habitat created with the intention of constructing a marina (Puerto Amor) and the natural habitats surrounding the Cabo de la Huerta area in Alicante (Spain). Employing an asymmetric design and examining two temporal and spatial scales, we utilized visual censuses in snorkeling to gauge the abundance and size of fish species, alongside various parameters related to habitat complexity and heterogeneity. The overarching hypothesis is that fish populations associated with artificial habitats will differ in terms of abundance, biomass, species richness, and diversity compared to fish populations associated with natural habitats, due to changes in complexity and heterogeneity. The findings indicate a shift in fish assemblages; for example, the family Labridae showed differences between the two habitat types for several species. These changes were due to the influences of the Posidonia oceanica meadow and algae like Jania rubens; being influenced by biological variables such as Ellisolandia elongata, Oculina patagonica, and Sarcotragus spinosulus; as well as physical variables such as stones, gravel, and blocks. While there is evidence of alteration in fish assemblages due to changes in habitat structure, there is also an increase in richness (9 species/m2) and total abundance and biomass (1000 ind./m2 and 1700 g/m2, respectively) in the artificial habitat. Multivariate analyses reveal that the fish community in Puerto Amor is less homogeneous than the one in the natural habitat. However, these analyses also indicate an overlap between the communities of both habitats, suggesting substantial similarity despite the noted differences. Consequently, although the habitat alteration has impacted fish populations, it has not diminished abundance, biomass, or species richness. In conclusion, the artificial rocky habitat resulting from the construction attempt at Puerto Amor harbor has fish populations with ecological significance and its removal could lead to undesirable impacts in the area, as the fish assemblages have become well established.