The lagoon of El Bibane (Tunisia) is a Mediterranean coastal area that is affected by an increasing human impact. Thus, an estimation of its biodiversity and an ecological quality assessment are very urgent. This study investigates the meiofaunal and nematode communities of the El Bibane lagoon both from a taxonomic and a functional point of view. Nematodes were the dominant group as is common in brackish water systems. The nematode community was made up of 62 genera in 22 families. Xyalidae, Chromadoridae and Cyatholaimidae were the richest and most abundant families. The taxonomic composition and biodiversity of nematodes were comparable to those found in other European and Mediterranean transitional areas. Both meiofauna and nematodes showed a clear subdivision between marginal and central areas. The central stations, represented by fine sediments and higher amounts of organic carbon, seemed to be characterized by low meiofaunal densities, nematode diversity and a strong dominance of 1B and 2B trophic guilds. These trends could be related not only to the grain size and organic load, but also to a possible influence of tidal currents that can transport pollutants in the central area of the lagoon coming from the adjacent coastal areas. Shannon diversity and life strategies are not always in agreement in defining the ecological quality, but an overall worse ecological quality was detected especially at S6. The results of this study are an important starting point for the future monitoring of the potential and actual human impact on the El Bibane area over time.