The study of intermittent rivers is a critical and timely issue due to their worldwide increase, triggered by several causes including climate change. The need to understand the response of intermittent river biota to water intermittency led us to conduct this study using benthic diatoms collected in southern Portugal. Benthic diatoms were explored in terms of assemblages, diversity indices, the Specific Pollution Sensitivity (SPI) Index, functional metrics (i.e. ecological guilds and life-forms) and conservation status. We verified that changes in water physico-chemical characteristics were highly controlled by flow intermittency, which in turn is directly linked to meteorological variables (air temperature and precipitation). Changes in diatom assemblages reflect the aquatic regime of sites, changes in aquatic states through time and mesohabitats (dry biofilm, samples collected in pools or under flowing conditions). Species richness, on the other hand, did not reflect these differences, whilst Shannon diversity and Pielou's Evenness indices only reflected mesohabitat differences. The SPI distinguished sampling periods, and mesohabitats. The relative abundance of ecological guilds changed with aquatic states, with the low-profile guild dominating in eurheic and arheic conditions (except during Summer), being replaced by motile taxa in summer arheic conditions, reflecting increases in nutrient and siltation. The hypothesis that benthic diatom assemblages in dry biofilm can be used as an indicator of ecological status during the dry-phase was validated, since no differences between the Ecological Quality Ratio determined in dry biofilm collected in Summer 2017 and the previous Spring 2017 in flowing water. A method is proposed for diatom sampling in dry biofilm, contributing to an integrated ecological status evaluation, which considers the dry-phase and enhances the reach of biomonitoring programs.