Dryland rivers in North Africa are undergoing significant physicochemical (anthropogenic pollution and salinity) and hydromorphological alterations, currently exacerbated by climate change. These changes threaten biota, ecosystem functions, and services, increasing their susceptibility to degradation. The Drâa river basin (southeastern Morocco) is an example of a river facing such pressure, leading to a reduction in flow and an increase in water salinity. This study investigated the composition, structure, diversity, and biomass of benthic microalgal and cyanobacterial communities in this intermittent river in relation to water salinity during dry and wet periods, using morphological and molecular identification. The results indicated a progressive increase in water salinity from the upper to the lower Drâa river, with the highest concentrations observed during the dry periods. Biofilm biomass was lower during wet periods, particularly at freshwater sites. Green algae and diatom biomass (measured as chlorophyll a per cm2 using a BenthoTorch) showed no significant response to salinity, while cyanobacteria preferred brackish water during dry periods. Alpha diversity was not affected by hydrological periods and salinity, though the diatom beta diversity was related to salinity changes. Halophilic and euryhaline taxa were prominent in brackish and saline waters, while oligohaline taxa prevailed in freshwaters. Our results stress that salinity and hydrological period affected the benthic algal and cyanobacterial assemblages in the Drâa river, and provide valuable information to identify environmental impacts.