The widespread impact of bottom towed fishing gear on benthic species and communities has long been recognized. The responses to a given intensity of fishing disturbance can be influenced by the extent to which these species and communities are preconditioned to disturbance by natural processes, in particular waves and currents. The advent of vessel monitoring system (VMS) and models of natural disturbance enable high-resolution and large-scale comparisons of fishing and natural disturbance. VMS data were employed to estimate the trawled area per 12 km by 12 km grid cell. We then quantified natural disturbance by estimating the number of days in a year the seabed was disturbed by tides and waves. As natural disturbance acts on large spatial scales, we assumed that each natural disturbance event affects whole grid cells. Frequencies could thus be translated into an area of impact, allowing us to compare fishing with natural disturbance. We show how such comparisons can be used to estimate the extent of different seabed substrate types significantly affected by demersal fishing. A measure of the probability that fishing disturbance exceeds natural disturbance provides one metric for identifying areas of significant trawling impact on seabed habitats and might be used to measure progress towards achieving good environmental status for sea-floor integrity within the context of the European Union's Marine Strategy Framework Directive. For more than half the seabed in the English sector of the Greater North Sea, the results suggest that disturbance attributable to demersal fishing exceeds natural disturbance based on data from the years 2006 to 2008. The imbalance between natural and fishing disturbance is greatest in muddy substrates and deep circalittoral habitats.