Marine protected areas (MPAs) are important conservation tools that can support the resilience of marine ecosystems. Many countries, including Canada, have committed to protecting at least 10% of their marine areas under the Convention on Biological Diversity’s Aichi Target 11, which includes connectivity as a key aspect. Connectivity, the movement of individuals among habitats, can enhance population stability and resilience within and among MPAs. However, little is known about regional spatial patterns of marine ecological connectivity, particularly adult movement. We developed a method to assess and design MPA networks that maximize inferred connectivity within habitat types for adult movement when ecological data are limited. We used the Northern Shelf Bioregion in British Columbia, Canada, to explore two different approaches: 1) evaluating sites important for inferred regional connectivity (termed hotspots); and 2) assessing MPA network configurations based on their overlap with connectivity hotspots and interconnectedness between MPAs. To assess inferred connectivity via adult movement, we used two different threshold distances (15 km and 50 km) to capture moderate home ranges, which are most appropriate to consider in MPA design. We applied graph theory to assess inferred connectivity within sixteen habitat and depth categories (proxies for distinct ecological communities), and used novel multiplex network methodologies to perform an aggregated assessment of inferred connectivity. We evaluated inferred regional connectivity hotspots based on betweenness and eigenvector centrality metrics, finding that the existing MPA network overlapped a moderate proportion of these regional hotspots, and identified key areas to be considered as candidate MPAs. Network density among existing MPAs was low within the individual habitat networks, as well as the multiplex. This work informs an ongoing MPA planning process, and approaches for incorporating connectivity into MPA design when data are limited, with lessons for other contexts.