The salt marshes of the Empordà wetlands are subjected to both physical variability, caused by hydrological fluctuations, and nutrient variability. We assessed which of these sources of variability most influenced nematode assemblages in 5 basins in the wetlands. One of these basins was permanently inundated, but the hydroperiods of the others were variable. Taxonomic composition and the Maturity Index, which is based on the ecological characteristics of nematodes (r- or K-strategists), were used to describe the assemblages. Variation decomposition analysis showed that nematode assemblages of the Empordà wetlands were more influenced by physical variability (18.2% of explained variation), caused by changes in variables such as conductivity and granulometry, than by nutrient variability (3.4% of explained variation). The Maturity Index of the assemblages was related to hydrological disturbance, but not to eutrophy. Cluster analysis based on taxonomic composition separated the permanent basin from the temporary basins. Nematode diversity and genus richness were significantly higher in the permanent basin than in the temporary basins. We conclude that the Maturity Index is valid for assessing hydrological disturbances in fluctuating Mediterranean environments, whereas assemblage parameters such as diversity and richness may not be because they responded to water permanence but not to other environmental factors associated with hydrologic variability.