The importance of environmental heterogeneity in lotic ecosystems is well recognised in river management, and continues to underpin studies of hierarchical patch dynamics, geomorphology and landscape ecology. We evaluated how physical characteristics and water chemistry measurements at high spatiotemporal resolution define channel units of potential ecological importance along 134 km of the lower Waikato River in North Island, New Zealand. We used multivariate hierarchical clustering to classify river reaches in an a priori unstructured manner based on (i) high-frequency, along-river water quality measurements collected in four seasons and (ii) river channel morphology data resolved from aerial photos for 1-km long reaches. Patterns of channel character were shaped by the depth and lateral complexity of constituent river reaches, while water quality patterns were represented by differences in clarity, chlorophyll fluorescence and specific conductance driven by tributary inflows in the mid-section of the river and tidal cycles in the lower section. Management units defined by physical characteristics or water quality did not necessarily align with boundaries typically reflecting clinal processes (e.g. tidal influence) or geomorphic, network or anthropogenic discontinuities. The results highlight the dynamic spatial and temporal properties of large rivers and the need to define clear objectives when deriving spatial units for management and research. Given that actions and targets for physical channel and water quality management may differ, the spatial extent identified for each of these does not necessarily need to directly coincide, although both should be considered in decision making and experimental design.