Many important marine ecosystem functions, goods and services rely on healthy, productive benthic communities, yet these communities are at risk from anthropogenic activity such as bottom fishing and aggregate dredging. Marine spatial management measures such as marine protected areas could help protect benthic communities from these activities and ensure the continued provision of the ecosystem goods and services that they support. The establishment of MPAs to protect benthic communities could be prioritised based on benthic invertebrate production, an indicator of benthic ecosystem quality that is comparable across different habitats. This thesis has considered the development and utility of modelled benthic infaunal production as a practical selection criterion for MPA design in the Irish Sea. The ability to model production over large scales and the spatial association between production and biodiversity have been investigated to determine whether or not benthic production can be and needs to be explicitly included as a selection criterion in MPA design to ensure protection from anthropogenic activities such as fishing. Results indicate that an empirical, size-based model that incorporates strong environment-production relationships can successfully predict relative benthic infaunal production over large scales in the Irish Sea. The model can also investigate bottom fishing impacts and the subsequent recovery of benthic production and biomass, all of which have utility for informing MPA design. A lack of spatial association between benthic production and biodiversity suggests that sites where the protection of biodiversity and production could be achieved simultaneously are limited in number, and therefore marine ecosystem function needs to be explicitly included as a selection criterion in MPA network design to ensure protection from anthropogenic activities. The implications of results for the spatial management of benthic communities are discussed, and general recommendations for MPA network design are made.