In this paper, we present a review and conceptual design to integrate hydrological/ecological models, global uncertainty and sensitivity analysis, integrative modelling and decision analysis for complex and adaptive transboundary challenges. The research uses the transboundary issues within the Okavango River basin, a shared water resource among the nations of Angola, Namibia and Botswana, as an example for constructing these integrated tools. The objective of this paper is to present a design that integrates a set of tools that builds systematically on past basin modelling research to incorporate the inherent uncertainty within the system and its application for answering practical management questions. Keywords: Okavango River basin, uncertainty analysis, AM, adaptive management, global sensitivity analysis, QnD model, decision analysis, hydrological modelling, ecological modelling, Angola, Namibia, Botswana, river basin modelling, transboundary water resources, risk assessment.