Inundation and drying in intermittent alluvial river reaches represent « temporal ecotones » between aquatic and terrestrial states, but have been surprisingly poorly explored by ecologists. In these rivers, desiccation-resistance and behavioral responses of taxa during drying/rewetting are likely to be the primary factors controlling the structure of hyporheic communities. Along the corridor of the Selwyn river, New Zealand, we explored i. in-situ hyporheic communities by sampling repeatedly sites scattered along a 7-100 % flow permanence (FP; the proportion of time that flowing water is present in a given period) gradient; ii. desiccation-resistance of taxa by artificially inundating bed sediments that had remained continuously dry for 1 to 300 days; and iii. taxa responses to artificial laboratory drying experiments. FP was a strong driver of hyporheic communities in the Selwyn river: density, diversity, and stability of communities decreased, and their composition varied, with FP. The onset of flow in dry-riverbed sediments simulated in the laboratory led to the appearance of aquatic invertebrates in all samples after 17 days, but community varied with the length of the preceding dry period. Drying experiments revealed that taxa resisted desiccation for >5 days under humid conditions (~85% RH) , while dry conditions (~40% RH) constrained resistance in all taxa studied. Our results suggest that bed sediments of intermittent reaches are privileged locations for terrestrial-aquatic interactions and that temporal ecotones of a about a week seem to exist between alternating terrestrial and aquatic states.