Matrix approaches are useful for linking ecosystem services to habitats that underpin their delivery. Matrix applications in marine ecosystem services research have been primarily qualitative, focusing on ‘habitat presence’ without including other attributes that effect service potential. We developed an evidence-based matrix approach of Ecosystem Service Potential (ESP) for New Zealand benthic marine habitats, and used two marine reserves to demonstrate that integrating information on the spatial extent and quality of habitats improved ESP evaluation. The two case studies identified substantial spatio-temporal variability in ESP: within one reserve, specific ESP showed an approximately 1.5-fold increase in the 29 years following protection. A comparison of two reserves found that the spatial extent of habitats contributing to the medicinal resources and waste-water treatment were 5 and 53 times greater respectively in one relative to the other. Integrating habitat area and quality with the ESP matrix improves on previous marine matrix-based approaches, providing a better indication of service potential. The matrix approach helps to communicate the non-market value of supporting and regulating services and can be used by resource managers to identify and track the potential for benefits derived from benthic marine habitats within existing, or new, marine protected areas.