Globally, ecosystems are experiencing increasing pressure from anthropogenic stressors. Human population growth is responsible for overexploitation of natural resources, pollution, land alteration and climate change. A change in landscape connectivity, may not only reduce the habitable space for species, but may also affect their movement and population dynamics. These changes potentially reduce the resilience of ecosystems against other stressors. Reserves are a common method to protect areas from overexploitation and habitat destruction and help to safeguard ecosystem functioning. Reserve size, location and configuration influence the effect of reserves and the optimal design of protected areas is a field of ongoing research. Connectivity is a guiding principle in protected area planning but the explicit incorporation of connections remains a challenge. Reasons can be found in the scarcity of quantitative data on connectivity and a lack of agreement on connectivity measures. Currently, connections in marine landscapes are less studied than on land. The aim of this thesis was to examine the relationship between connectivity and ecosystem processes, and to test methods for modelling and incorporating quantitative data on connectivity in the design of marine protected areas.