Understanding the effects of ecological disturbances in coastal habitats is crucial and timely as these are anticipated to increase in intensity and frequency in the future due to increasing human pressure. In this study we used directed kelp trawling as a scientific tool to quantify the impacts of broad-scale disturbance on community structure and function. We tested the ecosystem- wide effects of this disturbance in a BACI design using two 15 km2areas. The disturbance had a substantial impact on the kelp forests in this study, removing 2986 tons of kelp and causing a 26% loss of total kelp canopy at trawled stations. This loss created a 67% reduction of epiphytes, an 89% reduction of invertebrates and altered the fish populations living within these habitats. The effect of habitat loss on fish was variable and depended on how the different species used the habitat structure. Our results show that large-scale experimental disturbances on habitat-forming species have ecological consequences that extend beyond the decline of the single species to affect multiple trophic levels of the broader ecosystem. Our findings have relevance for understanding how increasing anthropogenic disturbances, including kelp trawling and increased storm frequency caused by climate change, may alter ecosystem structure and function.