SummaryWell‐designed marine protected area (MPA) networks can deliver a range of ecological, economic and social benefits, and so a great deal of research has focused on developing spatial conservation prioritization tools to help identify important areas.However, whilst these software tools are designed to identifyMPAnetworks that both represent biodiversity and minimize impacts on stakeholders, they do not consider complex ecological processes. Thus, it is difficult to determine the impacts that proposedMPAs could have on marine ecosystem health, fisheries and fisheries sustainability.Using the eastern English Channel as a case study, this paper explores an approach to address these issues by identifying a series ofMPAnetworks using the Marxan and Marxan with Zones conservation planning software and linking them with a spatially explicit ecosystem model developed in Ecopath with Ecosim. We then use these to investigate potential trade‐offs associated with adopting differentMPAmanagement strategies.Limited‐takeMPAs, which restrict the use of some fishing gears, could have positive benefits for conservation and fisheries in the eastern English Channel, even though they generally receive far less attention in research onMPAnetwork design.Our findings, however, also clearly indicate that no‐takeMPAs should form an integral component of proposedMPAnetworks in the eastern English Channel, as they not only result in substantial increases in ecosystem biomass, fisheries catches and the biomass of commercially valuable target species, but are fundamental to maintaining the sustainability of the fisheries.Synthesis and applications. Using the existing software tools Marxan with Zones and Ecopath with Ecosim in combination provides a powerful policy‐screening approach. This could help inform marine spatial planning by identifying potential conflicts and by designing new regulations that better balance conservation objectives and stakeholder interests. In addition, it highlights that appropriate combinations of no‐take and limited‐take marine protected areas might be the most effective when making trade‐offs between long‐term ecological benefits and short‐term political acceptability.