River systems provide diverse ecosystem services (ES), such as flood regulation (regulating), fresh water (provisioning), nutrient cycling (supporting), and recreation (cultural), among others. The construction of infrastructure (e.g., for hydropower, irrigation) enhances the delivery of tangible ES for example food or energy (generally provisioning) to meet human needs. However, the resulting change to river flows threatens both the ecological health of a river and its ability to provide intangible but vital ES, for example those which support the delivery of other services. Understanding these supporting ES processes in river systems is essential to fully recognise the impact of water resources development on ES delivery. Whilst approaches for assessing instream supporting ES are under development, to date few provide quantitative methods for assessing delivery. Thus, this paper sets out a framework for the assessment of instream supporting ES using hydroecological modelling. It links supporting ES delivery to fluvial hydrological indicators through the use of ecologically relevant hydrological indices and macroinvertebrate flow preferences. The proposed framework is demonstrated on the Beas River basin (Western Himalayas, India), and is flexible enough to be transferred to a basin-wide model, thereby allowing ES relationships to be accounted for in basin-wide water resources planning.