In Mediterranean streams, droughts and floods are mainly seasonal and predictable, occurring twice or three times a year. Under these conditions, multivoltinism and short life-cycles would be favoured, particularly for organisms with low migratory capacity. The meiofaunal community is therefore hypothesised to have species traits adapted to these hydrological perturbations. However, meiofauna have been neglected in many lotic studies. The present study examined the temporal variability of meiofaunal density and biomass over a 2-year period in three reaches of a low-order Mediterranean stream. Relationships between biological traits and hydrological and environmental characteristics were investigated. Resilience of meiofauna to floods was quantified using regression. Small differences in basin drainage resulted in different responses. The abundance and resilience of the meiofauna were higher in the upstream reach than those in the downstream communities. A small, worm-shaped body and active locomotor structures conferred higher resilience in the face of natural hydrological disturbances. Low-order reaches are refugia for functionally important meiofauna that can eventually repopulate downstream reaches.