To provide information necessary for a license application for a deep repository for spent nuclear fuel, the Swedish Nuclear Fuel and Waste Management Co. has started site investigations at two sites in Sweden. In this paper, we present a strategy to integrate site-specific ecosystem data into spatially explicit models needed for safety assessment studies and the environmental impact assessment. The site-specific description of ecosystems is developed by building discipline-specific models from primary data and by identifying interactions and stocks and flows of matter among functional units at the sites. The conceptual model is a helpful initial tool for defining properties needed to quantify system processes, which may reveal new interfaces between disciplines, providing a variety of new opportunities to enhance the understanding of the linkages between ecosystem characteristics and the functional properties of landscapes. This type of integrated ecosystem-landscape characterization model has an important role in forming the implementation of a safety assessment for a deep repository.