A modified ECOSIM model was used to investigate the impact of establishing marine protected areas (MPAs) in ecosystems defined by existing ECOPATH models. The impact of MPAs of various sizes was simulated, and changes in biomass and catch over a range of years observed. The response of biomass and catch to MPA size depended on the time period examined. For some ecosystem groups, the initial response was negative, but for all groups there were increases after 10 years. The greater the biomass exchange rate across the MPA boundary, the larger the MPA required to increase biomass levels. Within the range of exchange rates simulated, the maximum increases in catch and overall biomass levels were reached when 20% of the system was protected.