In this study, the meiofaunal diversity in Lake Varano (southern Italy) is investigated in detail. Using a statistical approach, these data were coupled with the physicochemical parameters of the bottom water and the sediment characteristics in order to understand the factors influencing meiofaunal biodiversity distribution. The lake is selectively influenced by different factors, namely: organic matter and grain-size, as well as water salinity. Although these assemblages appear to be poorly diversified, the diversity index values are similar to those generally reported in other transitional environments. Relatively higher values of both meiofaunal and benthic foraminiferal diversity were found in front of the Capoiale channel and in the inner part of the lake. The meiofaunal assemblages are mainly dominated by nematodes, copepods, and turbellarians. The benthic foraminiferal assemblages comprise 18 taxa and are mainly represented by calcareous forms, suggesting a relatively low degree of confinement and, consequently, moderately restricted conditions. These assemblages are comparable to the Ammonia assemblages with Haynesina germanica that are characteristic of lagoons along the Mediterranean coasts. On the basis of these findings, coupled with the biotic data, the lake can be regarded as an oligo-mesotrophic environment.