<p>Coastal lagoons, recognized as some of the most productive ecosystems, are also vulnerable to increasing human pressures, particularly due to the discharge of wastewater. This study aimed to evaluate, for the first time, the ecological status of the Marchica Lagoon (Mediterranean coast of Morocco). An integrated ecological monitoring approach, based on spatial diversity models of species assemblages (analyzed using taxonomic indices, structural trophic guilds as indicators of functional biodiversity, and marine biotic indices), was conducted in relation to sedimentary and hydrological descriptors. Water movements in the lagoon, such as currents and river waters, influence sediment distribution and create differences between stations close to pollution sources and those further away. This explains 66% of the observed variations in species living at the bottom of the water. dbRDA-DistLM analyses showed that water temperature, turbidity, and sediment type (such as mud, sand, and silt) are the main factors affecting species distribution. Stations near pollution sources are characterized by more silt and lower oxygenation, while those farther away show greater sediment diversity and better water quality. In total, 184 species from six taxonomic groups were recorded. The results revealed generally good to high ecological quality for most stations according to five biotic indices (AMBI, BENTIX, <InlineEquation ID="IEq1"> <EquationSource Format="TEX">\(H'\)</EquationSource> <EquationSource Format="MATHML"><math> <msup> <mi>H</mi> <mo>′</mo> </msup> </math></EquationSource> </InlineEquation>, M-AMBI, and ITI). However, five stations located on the continental edge were classified as moderate, highlighting the persistence of environmental pressures despite restoration efforts, such as the opening of a new maritime passage and the installation of wastewater treatment stations.</p>