Moroccan lagoons are highly productive and diverse ecosystems, vital for biodiversity, tourism, aquaculture, and coastal protection. However, they face increasing threats from human activities and natural pressures, jeopardizing their ecological integrity. The objective of this bibliographical review was to assess the ecological significance and potential for sustainable aquaculture development of six major Moroccan lagoons: Nador and Smir (Mediterranean coast) and Moulay Bousselham, Sidi Moussa, Oualidia, and Khenifiss (Atlantic coast). We delved into their geographical and morphological contexts, physico-chemical and hydrodynamic characteristics, heavy metal contamination levels, and biological diversity. Our findings revealed diverse environmental conditions across the lagoons, impacting their biological communities. Notably, Oualidia and Khenifiss exhibited a high resemblance in species composition, dominated by mollusks, while Nador and Sidi Moussa share similarities with crustaceans as the prominent group. Smir and Moulay Bousselham displayed distinct profiles, with crustaceans being the most abundant. Heavy metal contamination varied significantly, with Nador and Khenifiss showing the highest levels. Despite their ecological importance, most lagoons experience anthropogenic pressures that impact their ecological integrity. This review highlights recommended aquaculture species for these lagoons, with a primary focus on shellfish and fish farming, as well as the high suitability for seaweed cultivation, particularly Gracilaria. Emphasizing the need for sustainable management strategies, it underscores the crucial role of Moroccan lagoons as potential hubs for integrated aquaculture.