This study describes a new convenient and robust system developed to measure benthic boundary layer properties, with emphasis placed on the determination of bed shear stress and roughness height distribution within estuarine systems by using velocity measurements. This system consisted of a remotely operated motorised traverser that allowed a single ADV to collect data between 0 and 1 m above the bed. As a case study, we applied the proposed traversing system to investigate bottom boundary layer (BBL) hydraulic properties within Coombabah Creek, Queensland, Australia. Four commonly-employed techniques: (1) Log-Profile (LP); (2) Reynolds stress (RS); (3) Turbulent Kinetic Energy (TKE); and (4) Inertial Dissipation (ID) used to estimate bed shear stresses from velocity measurements were compared. Bed shear stresses estimated with these four methods agreed reasonably well; of these, the LP method was found to be most useful and reliable. Additionally, the LP method permits the calculation of roughness height, which the other three methods do not. An average value of bed shear stress of 0.46 N/m2, roughness height of 4.3 mm, and drag coefficient of 0.0054 were observed within Coombabah Creek. Results are consistent with that reported for several other silty bed estuaries.