The higher taxonomic structure of the meiofaunal community was investigated in three eastern Mediterranean lagoons, an open (Vassova), a semi-closed (Piges) and a closed lagoon (Alykes Kitrous). In total, 22 stations representing characteristic features in each lagoon were sampled. Stations were found to support a maximum of 19 meiofaunal taxa with densities ranging from 1 to 10,000 individuals per 10 cm2. Nematodes were dominant at all sites (30–97%) except at the hypersaline sites, where ciliates outnumbered all metazoan meiofaunal taxa (53–77%). Uni- and multivariate analyses were applied to study the community structure. The number of taxa and the meiofaunal density showed strong spatial differences in all three lagoons; however, the main source of variation occurred between the semi-closed and closed lagoons. Both the meiofaunal composition and density were significantly less at the hypersaline sites which had salinity above 100 psu. The meiofaunal distribution pattern was shown to be controlled by abiotic factors, in particular vertical stratification of salinity, bottom water currents and oxygen availability at the bottom water–sediment interface. However, the distribution of feeding resources (e.g. cyanobacteria, phytodetritus) was also found to play a key role in structuring meiofaunal communities.