The role of Work Package 3 within the REPAiR project is to develop and implement territorial metabolism models. The aim is to analyse, describe and model the case study areas with their subsystems and processes that define the area’s current metabolic patterns, from the vantage point of waste production and waste management. The interrelated domains place, flow & stocks, and behaviour & governance are taken into account with regard to spatial (where?),contextual (what, why, who and how?) and temporal (when?) dimensions. This deliverable – D3.1 – provides an introduction to the methodology for integrated spatial (Task 3.1), material flows (Task 3.2) and social (Task 3.3) analyses. It explains methodological considerations and choices, whilst laying out the approach, developed in close conjunction with the two main pilot case studies Amsterdam and Naples. Subsequently, this handbook provides guidelines for application in the four other case study areas. Task 3.1, concerning the spatial analysis, is located between the investigation of the flows that cross, and are processed within, our urban and peri-urban territories on the one hand, and the study of the spatial effects that these ‘metabolisms’ have on the territory, on the other. A core aspect of Task 3.1 is related to the identification of what REPAiR defines as ‘Wastescapes’. In Task 3.2 of WP3, Material Flow Analysis is used as a tool to study the material flows and stocks of the subsystems of the six case studies, based on consumption patterns and waste production. By introducing a new method for MFA, “Activity-based Spatial Material Flow Analysis” (AS-MFA), specific activities relating to material flows and stocks from waste production in subsystems, the involved actors and their interrelations can be identified. The AS-MFA aims to connect the spatial, material and social analyses in REPAiR. Task 3.3, on social analysis, is dealing with the linkages between sociocultural features and social sensitiveness about general environmental issues, and particularly about waste and resource management. Task 3.3 has a multilevel scope: secondary sociocultural inquiries are focusing on national level specificities, while the primer sociocultural stage of the research and the socioeconomic investigation is done on a local level. The representation and process models developed in WP3 have strong ties with WP4, regarding sustainability impact assessment and evaluation models, and with WP5 concerning eco-innovative solutions and change strategies. Moreover, the models are used as input to the GDSE (WP2) and inform –and are informed by –WP6 with regard to decision models. These interrelations accentuate the importance of common agreements regarding e.g. delineations, data sourcing and processing. Such issues are dealt with in this handbook, whilst underlining the necessity for continuing alignment between work packages of the REPAiR project.