Huvadhoo Atoll is a little-known and generally uncontaminated atoll of the southern Maldives, although the human pressure is increasing. This study represents the first attempt to characterize the meiofaunal and nematode assemblages of its lagoon both from a taxonomic and functional point of view. The nematode assemblage was made up of a total of 131 genera in 33 families. Desmodoridae, Chromadoridae and Xyalidae represented the richest and most abundant families, followed in terms of abundance by Selachinematidae and Comesomatidae. The nematode richness was overall higher than that reported in the previous studies carried out in the Central part of the archipelago. The diversity patterns revealed higher values than those reported for the back-reefs platforms, so confirming the positive influence of the water depth on the biodiversity of the nematode assemblage. The statistical analysis highlighted a significant taxonomic difference of the assemblages between the stations characterized by fine and medium-coarse sands, respectively, in line with the auto-ecological preferences of the taxa detected. The use of some nematode descriptors for assessing the ecological quality status (EQS) of the lagoon has revealed a slight disturbance in the station close to Viligili, one of the most urbanized islands. However, the summarization of all the descriptors used allows the highlighting of the good EQS of the Huvadhoo lagoon. Thus, the results of this study may be taken as the starting point for the future monitoring of the potential and real impact of the anthropogenic activity on the area over time.