The structure of the bottom boundary layer (BBL) in aquatic flows influences a range of biophysical processes, including sediment transport, hyporheic exchange, and biofilm formation. While the structure of BBL above bare sediment beds has been well studied, little is known about the complex near-bed flow structure within canopies of aquatic vegetation. In this study, we used high-resolution laboratory measurements and numerical Large Eddy Simulations to investigate the near-bed mean and turbulent flow properties within staggered-ordered emergent canopies under a wide range of flow and canopy conditions. There is strong horizontal variability of key near-bed flow characteristics on the scale of the vegetation elements. Measurement locations that provide single-point flow characteristics closest to the spatially-averaged values were identified. The spatially-averaged BBL thickness is influenced strongly by canopy density. This impact of canopy density is engendered through its direct control of near-bed turbulent kinetic energy (TKE), which in turn is negatively correlated with BBL thickness, both locally in a given flow and across the range of flow conditions studied here. A model based on the near-bed TKE is developed to predict the BBL thickness and, ultimately, the bed shear stress. The strong agreement between model predictions and experimental data may explain why both TKE and bed shear stress may be seen as drivers of sediment transport processes in vegetated flows. These findings provide new insights into the physical links between near-bed flow variables and therefore contribute to the understanding of some of the complex biophysical processes present in vegetated flows