Sustainable river management requires a thorough understanding of the response of aquatic biota to riverine microhabitat variability. The purpose of this study was to assess macroinvertebrate hydraulic-habitat suitability in Ecuadorian Andean rivers to support habitat modelling for sustainable ecosystem management. 597 macroinvertebrate samples were collected from ten sampling stations the Yanuncay River, Ecuador. Physical, chemical, hydraulic and habitat variables were measured/calculated. Froude number, Reynolds number, substrate index and algae coverage were major drivers of macroinvertebrate response, and were used to develop suitability curves for Baetodes, Andesiops, Camelobaetidius, Ecuaphlebia, Anacroneuria, Atopsyche, Simulium and Palpomyia using General Additive Models. Standardised density contours of taxa as functions of hydraulic and habitat variables were also developed. Taxonomic response was related to body structures/shapes and feeding habits. Baetodoes, Simulium, Anacroneuria and Atopsyche preferred fast flowing waters, and thus, they could be significantly affected in case of flow reduction. Similar habitat suitability curves were developed from the main river and the tributaries, possibly due to the short distance between the sampling stations. This study fills a major knowledge gap by developing macroinvertebrate habitat suitability curves for future physical habitat simulations and environmental flow assessments in the Andean region.