Agricultural systems and problems of sustainability are complex, covering a range of organisational levels and spatial and temporal scales. Integrated assessment (IA) and modelling (IAM) is an attempt to capture complex multi-scale problems. Scale changes and model linking methods (referred to as scaling methods) are important in dealing with these problems but they are often not well understood. The present study aims to analyse scaling methods used in the recently developed multi-scale IA model SEAMLESS-IF which is applied to two case studies of complex agri-environmental problems. The analysis is based on a classification of up- and down-scaling methods which is extended for the purpose of this study. Our analysis shows that scale change...