This study was conducted in Lake Varano (southern Italy) in order to determine the environmental parameters that influence nematode taxonomic and functional diversity and how they influence them, and to classify for the first time the ecological quality status of a transitional environment. The general composition and level of taxonomic diversity were comparable with those reported for transitional environments worldwide. Principal component analysis revealed that the main environmental factors controlling the assemblages in terms of both composition and biological traits were grain size, organic matter, pollution load index and, only secondarily, salinity. Molgolaimus allgeni, Terschellingia longicaudata and Leptolaimus luridus showed higher values in relation to silt, organic matter and pollution load index, while Axonolaimus caudostriatus, Odontophora wieseri, Paramonhystera pellucida and Paracanthonchus longicaudatus showed higher values in relation to the redox potential and sand percentage. Salinity was detected as an influencing parameter only secondarily and particularly for Calomicrolaimus honestus, Daptonema normandicum, Thalassomonhystera parva and Sabatieria pulchra. With respect to functional traits, the trophic groups seemed to be mainly related to sediment type, which is in turn reflected by the nature of the available food. The maturity index, as well as c-p classes, did not always permit a clear interpretation of the interaction between anthropogenic and natural factors. However, the greater influence of the San Antonino and San Francesco Canals was perfectly revealed by the nematode assemblage. In accordance with the current ecological quality classes, Lake Varano can mainly be classified as having good to poor ecological quality status.