Rivers and streams affected by mining activities often receive short-term sharp salinity increases due to water-soluble stockpiled materials being washed into receiving water bodies. We conducted a mesocosm study to explore the response of structural (diatom and stream invertebrate communities) and functional descriptors (chlorophyll a concentration, fungal biomass and leaf decomposition) to repeated short salinity pulses (3h of duration, with nominal electrical conductivities of 5, 10 and 15mScm−1), mimicking the exposure pattern occurring at salt-mine affected rivers. The experiment was conducted in 12 artificial flow-through stream systems over 16days. The effect of the salt pulses on the ecosystem structure and functioning did not fully match most of our initial hypotheses, with the community response being weaker than predicted. The diatom community was, however, dominated by salt-tolerant species throughout the experiment, showing no consistent response to the treatment. The invertebrate response was associated with statistically significant changes in community structure (i.e. abundance of the different taxa) but no statistically significant changes in taxa richness. The salt pulses affected some functional descriptors of the ecosystem: fungal biomass exhibited a unimodal response to treatment magnitude, algal growth (i.e. chl a biomass) was hampered with increasing conductivity and leaf decomposition was significantly reduced in the high treatment. •We explore the response of stream ecosystems to repeated short salinity pulses.•We studied chlorophyll a, fungal biomass, leaf decomposition, diatoms and invertebrates.•Only fungal biomass, and invertebrate and shredder density showed significant responses.•Overall treatment effect did not increase following repeated pulses or with treatment magnitude.•Overall, the ecosystem response was weaker than that reported for press exposure.