Bizerte lagoon is a valuable socio-economic ecosystem which is renowned for its significant biodiversity and its strategic position in the Mediterranean and in northern Tunisia. It is characterized by an important biodiversity and a high biological productivity, which makes of it a nursery for several marine species. It is also a place of brood stock maturation for others and a feeding area for many migratory species. Its shores and maritime space host lots of human activities, such as coastal fishing, shellfish farming, maritime traffic, recreational fishing and nautical sports, besides 277 industries spanning several sectors of activity such as leather and textile as well as the refining of hydrocarbons and the steel industry. These activities cause severe pollution and result in many anthropogenic disturbances. The aim of this work is to study the sanitary state of Bizerte Lagoon using a biological and ecosystem approach that exploits bio-ecological indicators at the scale of specimen, population, community or whole ecosystem. The findings of this study have revealed the following facts: the peri-lagoon part of the Northeast zone is distinguished by an interesting biological diversity. According to statistical descriptors, the most abundant and frequent zoological groups are gastropod mollusks followed by crustaceans. In terms of diversity indexes, the values obtained showed that the Northeast zone has a poor to mediocre ecological status. This research demonstrates that Bizerte Lagoon is undergoing an anthropic pressure that has been jeopardizing the biodiversity of this ecosystem.