This NEXOGENESIS Deliverable describes the methodological approaches to be employed within the System Dynamics Models (SDMs) for each of the five Case Studiesregarding: scenario analysis; sensitivity analysis; what-if testing; and uncertainty analysis. It outlines why these methods are essential for improved policy-relevant information. It describes how data provided through Work Package 2 will be exploited to assist is these analyses, how further work to be carried out in WP4 will utilise the uncertainty/sensitivity analyses in the Machine-Learning techniques, and how the results can be communicated to stakeholders via a visual decision support tool to be developed. The combination, robustness, and comprehensiveness of the techniques to be used in NEXOGENESIS for uncertainty and scenario analysis will lead to novel scientific and societal impact, and will greatly advance the current state-of-the-art in nexus-relevant research, especially once Machine-Learning methodologies are coupled with, and exploit, the analyses described in this Deliverable.