Disturbance may alter the resistance of communities to non-indigenous species as it frees space and removes competitively superior species. In a factorial field experiment we studied how different types of mechanical disturbance affected the biomass level of the non-indigenous amphipod Gammarus tigrinus in a brackish water charophyte community. Mechanical disturbance affected the biomass of G. tigrinus with a time lag between disturbance and response of the gammarid species. In general, all types of disturbance reduced gammarid biomasses. The effect persisted until the end of the experiment regardless of the recovery of macrophyte communities in terms of species number and biomass of benthic invertebrate and plant species. Thus, a possible cause of reduced biomass of the gammarid amphipods relates to the decreased biomass of Chara aspera and its structural changes. This indicates that the dominance of G. tigrinus in a low saline system has less to do with strong species interactions (e.g. competitive displacement) than with habitat-level processes (e.g. changes in habitat structural characteristics and food supply).