Over the last decade there has been a major rise in the number of attempts at fish conservation and management as a response to the widespread degradation of aquatic ecosystems. The assessments involved are rarely planned and executed with inputs from the species life history, particularly their microhabitat use over space and time. The seasonal and sizerelated microhabitat use of two critically endangered cyprinids -the Iberian nase Iberochondrostoma almacai and Iberian chub Squalius aradensis -was examined at seven sites across four small catchments in southwest Portugal. Both species displayed nonrandom microhabitat use. In autumn, nase preferred more sheltered (> 50 % cover) habitats with small substrata (organic cover and silt) than in summer, while chub were found to occupy significantly fasterflowing habitats areas (> 10 cm/s) with coarser substrata (> 50 mm particle size) in the spring than in the rest of the year. Size-related analyses indicated that young-of-year (yoy) nase used coarser substrata (> 5 mm particle size) and more exposed habitats (< 50 % cover) than adult nase. Adult chub, on the other hand, occupied coarser substrata (> 50 mm particle size) and faster-flowing areas (> 10 cm/s) than yoy and juveniles. Based on these findings, it was possible to assign the species to ecological guilds and to classify them as limnophilic (nase) and eurytopic and lithophilic (chub). Both species generally occupied distinct microhabitats, although resource-use overlap was significant in summer. During this season, overlap was found between yoy nase and chub, juvenile nase and juvenile/adult chub, and between adults of both species. The present study identified key factors in the species habitat requirements and helped develop management recommendations for river restoration that may have a wider application, particularly for other Mediterraneantype rivers.