The lagoon of Boughrara is the largest lagoon in Tunisia. For several decades it has been subject to the impact of increasing anthropogenic activities, and also to environmental stressors due to climate change and the low renewal of its waters. The present work is a contribution to the study of the functional organization of the benthic macrofauna of the lagoon of Boughrara 3 years after the extension of the channel ‘El Kantra’ which connects this lagoon to the open sea. In total, 13 stations facing the main prospective sources of disturbance and in areas likely to be more polluted were seasonally sampled during 2009–2010. Seasonal monitoring of the abiotic parameters shows a spatial heterogeneity linked to environmental and anthropogenic factors, including hydrodynamics, sedimentary texture and anthropogenic activities. The community of benthic macrofauna is generally poorly diversified at lagoonal-marine stations undergoing influences of both the marine and lagoon environment. The extreme seasons in terms of temperature and salinity seem to have an important role in the reduction of biodiversity in the lagoon of Boughrara. The trophic structure of the macrobenthic community is generally dominated by selective deposit feeders, and seems to be linked more to the availability of trophic resources than to disturbance.