Fish belonging to Gobiidae are well represented in the Marchica lagoon on the Moroccan Mediterranean coast, both in terms of species richness and abundance, with the black goby (Gobius niger Linnaeus, 1758) being the dominant species. The present study aims to examine (1) the ecological traits of Gobius niger and its environmental drivers in the lagoon and (2) the potential lagoon-related footprint using morphometric, genetic and parasitological proxies. Systematic sampling covering the whole lagoon basin performed between October 2015 and November 2016 revealed year-long presence of G. niger throughout the lagoon with significantly low densities in winter. The higher abundances were recorded in the shallow bottoms of the lagoon inner margins on a variety of substrates (mud, muddy-sand, sandy-mud and fine sand) mostly covered by macroalgae and/or seagrass meadows. Multivariate analysis evidenced that depth and temperature were the important predictor variables explaining the spatial distribution of G. niger in the lagoon, with depth being the best model explaining about 33% of the total variability. Comparison of black goby populations from the Marchica lagoon with their counterparts from the adjacent Mediterranean coast of Morocco revealed that specimens caught at the sea are of a bigger size compared to the ones from the lagoon without any effect of the colour morphs observed (dark vs clear). Of the 180 gobies investigated, not a single one hosted the parasites we targeted in the parasitological approach, monogenean flatworms. The absence of population structuring, low genetic diversity and presence of common haplotypes indicate no apparent restriction in the gene flow between the two populations. Moreover, the morphometric differences and colour morphs observed seems to be due to the external environment rather than genetic differences. Gobius niger plays a key eco-trophic role by providing a link between benthic invertebrates and large predators. Therefore, ultimately, the shallow beds of the lagoon, where the species is abundant, are key habitats in the Marchica lagoon and need to be considered in all management plans aiming at the conservation of biodiversity and ecological processes.