1. Methods for assessing habitat sensitivity to human impacts are needed to gauge the sustainability of existing impacts, develop spatial management plans and support meaningful environmental impact assessments. These methods should be quantitative, validated, repeatable and applicable at the scales of impact and management. 2. Existing methods for assessing the sensitivity of marine habitats to human impacts have tended to rely on expert judgement and/or scoring systems. They are neither validated, quantitative nor repeatable. 3. We have developed a method that meets the criteria for assessing the sensitivity of seabed habitats to physical disturbance, and delineating and mapping habitat sensitivity at large spatial scales (>105 km2). The method assumes that sensitivity is related to the recovery time of production or biomass, as predicted using a size-based model that takes account of the effects of natural disturbance. 4. As trawling disturbance is a major and widespread direct human impact on shelf seas, this was used as an example of anthropogenic physical disturbance. We mapped habitat sensitivity to trawling in 9-km2 boxes across an area of 125 000 km2 in the North Sea. 5. Habitat sensitivities varied widely, and a trawling frequency of 5 year-1 in the least-sensitive habitat had the same ecological effect as a trawling frequency of 0.3 year-1 in the most-sensitive habitat (based on production). When trawling effort was held constant but redirected to the least-sensitive habitats, the existing impacts on production and biomass were reduced by 36% and 25%, respectively. 6. Synthesis and applications. The method described in this paper enables managers to predict the implications of changing patterns of human impact on seabed habitats when establishing spatial management plans. In the context of fisheries management, this will support the identification and selection of fishing grounds that minimize the adverse ecological effects of fishing; the selection of closed areas (both representative and highly sensitive); the comparison of management options that might reduce the overall environmental impacts of fishing; and any future steps towards the application of environmental impact assessment in advance of fishery development.