Geometric modelling of river channel topography is a method of design synthesis wherein specific 2D geometric elements of river topography, such as the bed profile, cross sectional shape, and channel planform contours, are expressed mathematically in isolation and then combined to produce a 3D heightmap. We utilized the geometric modelling framework to synthesize channel terrains that reveal flow−form−function linkages to investigate what roles variability in bed roughness, thalweg elevation and channel width play in defining hydraulic and ecohydraulic conditions of a channel reach from baseflow to bankfull discharge. To achieve a robust inquiry for a range of settings, this study developed four distinct synthetic channel terrain models for each of three stream reaches of different channel types in the South Fork Eel River in northern coastal California, USA. To test the process-based effects of these diverse terrain synthesis options, we compared the resulting hydraulic patterns and preferred habitat availability for fry/juvenile steelhead trout and coho salmon over a range of discharges. Among thalweg bed undulation, width variation and bed roughness, we found thalweg bed undulation was the key factor affecting the channel ecohydraulic response at baseflow condition. At bankfull condition, thalweg bed elevation had the largest effect in high-order mainstem streams identified by gravelcobble dominated high width-to-depth riffle-pool sequences, width variation had the largest effect in mid-order confined channels with gravel-cobble, high width-to-depth ratio with expansions/contractions and bed roughness had the largest effect in low-order streams with low width-to-depth ratio, high-gradient, cobble-boulder and step-pool/cascade channels.