We studied benthic communities with different types of habitats in the Moulay Bousselham lagoon during the winter and summer of 2019. We aimed to investigate biodiversity trends across a scale of seasonal variation. The lowest water temperatures were recorded downstream. This reflects the influence of cold oceanic waters at the lagoon entrance while the salinity shows a decreasing gradient from downstream to upstream. Sediment analyses showed that the lagoon is mainly composed of sandy and silty sediments. In stations with vegetated habitats, the biomass of Zostera noltei seagrass ranged from 0.79 g dry weight (DW) to 46.69 gDW in winter and from 9.34 gDW to 47.67 gDW in summer, while the biomass of Ruppia cirrhosa seagrass ranged from 5.53 gDW to 28.66 gDW in winter and from 14.48 gDW to 34.06 gDW in summer. Apart from water temperature and salinity, environmental variables are not significantly different in winter and summer (ANOVA test: p > 0.05). In the 29 sampled stations we used, we found 42 taxa in winter and 32 taxa in summer with a mean biomass value of 25.10 g AFDW m−2 (winter) and 9.14 g AFDW m−2 (summer). Apart from biomass, which is subject to seasonal variations, diversity parameters are not significantly different from one season to the next (ANOVA test: p > 0.05). Results from DistLM analysis revealed that the diversity and distribution of benthic macrofauna in the Moulay Bousselham lagoon were controlled by a combination of factors: sediment characteristics (mud content, median grain size, total organic matter %, carbon %, CaCO3% and CO2%), water characteristics (temperature and salinity) and habitat type (biomass of Zostera noltei and Ruppia cirrhosa seagrasses).