This paper presents a methodological framework to estimate the likely cumulative impact on fragile benthic organisms from bottom fishing activity. The approach has been designed to facilitate standardised application among various gear types and areas to allow comparisons between fisheries employing different bottom fishing methods. New Zealand implemented this approach in its preliminary assessment of bottom fishing impacts for the 2008/09 toothfish longline fishery. This paper illustrates the utility of the standardised approach and provides a methodological template for systematic impact assessment in fisheries using bottom impacting methods, to inform mitigation efforts and as a necessary component of a full ecological risk assessment.