The article presents the contribution of the Department of Integrated Geography of the Adam Mickiewicz University in the development of methodological framework and practical applications within the concept of the social-ecological system. The ongoing work focuses on several research fields. They are: ecosystem services as benefits that people receive from the functioning of ecosystems; elements of green infrastructure with particular emphasis on urban agriculture and biodiversity and its references to natural and man-made conditions; as well as nature-based solutions, related to the use of the potential of natural features and processes in spatial development. The research and projects carried out serve to integrate the practical scientific sphere, and at the same time emphasize the necessity of a holistic view of the social-economic and natural system.