Background Mobile bottom fishing, such as trawling and dredging, is the most widespread direct human impact on marine benthic systems. Knowledge of the impacts of different gear types on different habitats, the species most sensitive to impacts and the potential for habitats to recover are often needed to inform implementation of an ecosystem approach to fisheries and strategies for biodiversity conservation. This knowledge helps to identify management options that maximise fisheries yield whilst minimising negative impacts on benthic systems. Methods/design The methods are designed to identify and collate evidence from experimental studies (e.g. before/after, control/impact) and comparative studies (spanning a gradient of fishing intensity) to identify changes in state (numbers, biomass, diversity etc.) of benthic biota (flora and fauna), resulting from a variety of mobile bottom fishing scenarios. The primary research question that the outputs will be used to address is: “to what extent does a given intensity of bottom fishing affect the abundance and/or diversity of benthic biota?” Due to the variety of gear and habitat types studied, the primary question will be closely linked with secondary questions. These include: “how does the effect of bottom fishing on various benthic biota metrics (species, faunal type, trait, taxon etc.) vary with (1) gear type and (2) habitat, and (3) gear type-habitat interactions?” and (4) “how might properties of the community and environment affect the resilience (and recovery potential) of a community to bottom fishing?”