Mobile bottom fishing is widespread and is known to impact seabed habitats. Risk assessments can evaluate these impacts and inform decisions about the certification of sustainable fisheries by bodies like the Marine Stewardship Council. Spatial risk assessments require input data layers of seabed habitats and fishing effort, and when available, they are often available at different resolutions (number of different habitat categories for seabed habitats, spatial cell size for fishing effort). Here we evaluate how the outcome of risk assessments of the impact of bottom trawling depends on resolution of these data layers. We evaluate the relative benthic state, recovery time and the resulting indicative score for the ‘habitats outcome’ of the Marine Stewardship Council (MSC) Fisheries Standard using three different levels of habitat categorisation and four different fishing effort resolutions for 14 areas in the North Sea that are intensely fished by different trawl gears. In this framework outcomes are reported by habitat category. The assessments show that when fishing effort is low, choices about effort and habitat resolution do not affect the scores. Fine and medium resolution habitat maps results in a larger range of seabed status and recovery times than coarse resolution maps, and worse predicted habitat outcomes. In MSC fishery assessments, both mean and minimum scores are important to achieving certification. The mean score for each Principle must be ≥ 80 for a fishery to be certified, with any score below 80 triggering conditions that must be addressed by the fishery within five years of certification. A single score below 60 prevents a fishery being certified. Coarser fishing effort resolution layers lead to higher seabed status and faster recovery times. As a result, more detailed data layers result in a larger range of MSC scores, including more scores that would result in conditions on certification and modifications to fishing practices. In conclusion, for intensely fished areas, more detailed data layers provide a more stringent assessment of the sustainability of bottom trawl fisheries and it is recommended that the most-detailed available fishing effort data and fine or medium scale habitat data is used in assessments.