Successful transfer and uptake of qualitative reasoning technology for modelling and simulation in a variety of domains has been hampered by the lack of a structured methodology to support formalisation of ideas. We present a framework that structures and supports the capture of conceptual knowledge about system behaviour using a qualitative reasoning approach. This framework defines a protocol for representing content that supports the development of a conceptual understanding of systems and how they behave. The framework supports modellers in two ways. First, it structures and explicates the work involved in building models. Second, it facilitates easier comparison and evaluation of intermediate and final results of modelling efforts. We show how this framework has been used in developing qualitative reasoning models about three case studies of sustainable development in different river systems.