In the context of an ecosystem-based approach to the management of marine resources, fisheries managers have to consider the effects of fishing impacts on seabed habitats to achieve sustainable use of marine resources. Bottom fishing, using mobile gears such as scallop dredges or otter trawls, impacts benthic habitats directly due to the need to maintain the gear in close contact with the seabed to maximize catches of target species. In this thesis, the loss of emergent epifaunal biomass due to fishing disturbance was quantified at the scale of an entire fishery. The results showed how fishing and the physical environment, i.e. substratum type and the overlying hydrodynamic regime, interact to determine the biomass and size composition of the resident emergent epifauna. A novel method was used to track the spatial movement of fishing vessels in the study and the implications of using alternate methods of fishing effort estimation to describe fishing impacts were analyzed. The results show that analytical methods (track reconstruction, density of position records) and the grid cell resolution used for the analysis can lead to the underestimation of fishing impact on epifaunal communities. This novel technique was then applied to enable the determination of the recovery of benthic communities of hard substrates. The recovery of species abundance, species composition and functional group structure was estimated to take from 1 to 4 years, and was significantly influenced by the prevailing hydrodynamic conditions. Finally, the application of a novel approach to monitoring habitat distribution and status was investigated. The technique utilized underwater imaging of a laser line applied to the seabed that allows the calculation of a habitat complexity index. Details of the implications of the various methods developed in this thesis and of the key findings to the implementation of an ecosystem approach to fisheries management were integrated in the general synthesis.