It is necessary to combine the understanding of physical environmental drivers with social, economic, cultural and political perspectives and information to build resilience to future flood and drought hazards. We present a flexible collaborative modelling approach to improve resilience to hydrological extremes in large basins with application to the Limpopo River Basin (LRB). It uses an iterative, knowledge co-production process to strengthen crucial bridges between scientists and water management stakeholders on the appropriate scale(s). In the proposed collaborative modelling approach, the integrated hydro(geo)logical model is combined with regional to transboundary people’s knowledges and policies. We analyse the effect and importance of stakeholders’ feedback on the numerical model prediction. The proposed methodology is applied in the Limpopo River Basin (LRB) where floods and droughts are recurrent events. Through this iterative multisector collaborative modelling approach, we aim to develop a reliable and feasible management instrument to help reduce the impact of alternating droughts and floods and increase the resilience to hydrological extremes.