Coastal lagoons are considered as one of the most productive ecosystems worldwide but are also vulnerable to the growing human-made stressors. This study aimed at assessing, for the first time, the ecological status of the Oualidia lagoon (Atlantic coast of Morocco) using benthic macroinvertebrates as bioindicators. An integrative ecological monitoring approach based on spatial diversity patterns of species assemblages (examined using taxonomic indices, structural trophic guilds as indicators of the functional biodiversity, and marine biotic indices) in relation to sedimentary and hydrological descriptors was performed. Results showed that hydrodynamic conditions, represented by intra-lagoon currents and the watershed, govern the entire sediment distribution within the lagoon and establish a longitudinal downstream-upstream gradient and transverse right-left banks, which explained 66% of the total variation observed in benthic assemblage composition. Seagrass meadows affect positively the abundance of dominant species but do not support high diversity. Overall, macrozoobenthos spatial pattern consists in modification of the relative abundance of species, independently of species composition. The average score of the ecological classes obtained from five biotic indices (AMBI, BENTIX, H’, MAMBI and ITI) showed an acceptable status of the benthic assemblages. This integrated analysis resulted in a holistic view of the benthic-ecosystem that will serve in implementing an ecosystem-based approach to the management of the Oualidia lagoon.