Reach-scale river restoration or environmental water allocation (EWA) exercises typically address the magnitude and temporal dynamics (frequency, duration, timing, rate of change) of flows required to sustain desirable ecological conditions along a river. The role of geomorphology in this process is to broaden the gaze beyond flows to consider larger and longer-term interactions between valley lithological structure, and the feed and fate of flow-sediment mixtures. This paper proposes the integration of numerical morphodynamic modelling in evaluations of environmental water requirements for non-perennial riverscapes (channel–riparian–floodplain environments). The paper presents a methodological framework, and proof of concept case study from the Touws River, South Africa, for the application of morphodynamic modelling in EWA. The paper illustrates operational approaches to modelling the complexity of dryland mixed bedrock-alluvial (and mixed-load) riverscapes with highly variable non-perennial flow regimes, including an approach to generating initial bed conditions for numerical experiments by ‘morphodynamic spin-up’, and approaches to synthesising and presenting numerical experiment output in the form of a dynamic range of potential variability in metrics of physical habitat suitability and diversity, and disturbance/renewal regimes. Such efforts can assist in enhancing field observations and testing field-based hypotheses of flow-sediment regime–physical habitat associations, extending the timescales of analysis beyond field observation, and constraining uncertainty about the dynamic range of variability in responses to predicted future flow-sediment regime modifications. Further research is needed to develop growth models appropriate for key non-perennial river vegetation types, to support biomorphodynamic modelling of geomorphology–vegetation interactions, and to determine or predict appropriate inlet sediment concentrations for historical and future modification scenarios.