Understanding the interactions between physical habitat and aquatic biodiversity has become a key research objective in river management. River research and management practitioners are increasingly seeking new methodologies and techniques for characterizing physical habitat heterogeneity. The physical biotope has been widely employed as the standard mesoscale unit in river surveys. However, few surveys have quantified the combined physical heterogeneity at the meso- and microscale scale via a single technique. This paper describes a new field methodology for assessing variations in hydraulic habitat and retention across different channel types (e.g. step-pool, bedrock, plane-bed and pool-riffle). Hydraulic habitat and retention was measured by timing 100 flow tracers across a 100-m stream length, and recording the types of trapping structures. The pattern of flow tracers and retention varied significantly between channel types and structures. Rocks (boulders and cobbles) were more important retentive structures than eddies and snags (woody material and vegetation). The results indicate the importance of a diverse hydraulic environment, woody material and channel substrate character in increasing physical heterogeneity within a stream reach. The findings suggest that the field methodology may be an effective tool to assess differences in physical heterogeneity pre and post river restoration activities.