Invasive gobies can have severe detrimental effects on local fish communities, however, direct methods for population control are often insufficient (i.e. fishing) or not feasible (i.e. poisoning). Indirect methods, such as habitat modifications in the course of restoration programs, appear promising but are poorly studied. In this study, we investigate the effects of different restoration measures on the abundance and occurrence of non-native gobies in the main stem of a free-flowing section of the Danube and attempt to disentangle these measures from general large-scale trends by applying a Before-After-Control-Impact design. We found three invasive goby species (racer, bighead, and round goby) in the sampling area, partly with very high abundances. Four to six years after the installation, the measures had negative (riprap removal), neutral (side arm reconnection), or positive (groyne field adaptations) effects on goby abundances. We conclude that the impact of the measures depends on the type of intervention, is species-specific, and is largely related to substrate composition. Independent from the effect of the measures, abundances of bighead and round goby dropped in the project and reference sections after the pre-survey. This general decline probably indicates a stabilization phase of the goby populations on a lower level, but may also be influenced by a major flood event. Nevertheless, our results indicate a high potential of shoreline modifications for invasive species control, calling for considering and incorporating them in river restoration programs.