The study focused on the compositional and trait changes in benthic diatom assemblages found in both permanent and intermittent lowland streams, coupled with their aquatic different aquatic phases (flowing, standing and dry) in the Carpathian Basin. Our results highlighted that the compositional separation of permanent and intermittent streams at both taxonomic and trait levels have already begun in the region. A clear compositional separation at both taxa and trait levels between the water phases could be detected even during a one-year study. Our results strongly emphasized the importance of regular and frequent monitoring of intermittent streams, as hydrological changes in these small streams do not take much time and occur quickly. Finally, it has to stress that very careful management strategies and protection are needed, as these lowland streams play a key role in ecosystem services such as agricultural irrigation, local “climate regulation” and recreational waters.