Sites with great potential for electricity generation from tidal stream energy are often characterized by high levels of turbulence and severe wave climates. These characteristics are known to substantially increase turbine blade loadings fluctuations, which may lead to premature device failure and blade fatigue. In order to be commercially competitive, tidal energy devices must function in turbulent environments for approximately 25 years without requiring major maintenance operations. Hence, knowledge of turbulence parameters prior to device deployment is crucial to avoid unnecessary costs with overengineering and maintenance. Aiming to support the development of tidal energy in Australia, the Tidal Energy in Australia (AUSTEn) Project identified two sites with potential for tidal energy: Banks Strait, Tasmania and Clarence Strait, Northern Territory. The datasets presented here reveal high-frequency current velocity measurements taken throughout the water column with Nortek Signature new generation Acoustic Doppler Current Profilers (AD2CPs) at one measurement station in Banks Strait and two in Clarence Strait. Measurement periods are between 2 and 3 months, which are significantly long deployment periods for turbulence characterization in tidal energy sites compared to other datasets available in the literature. Processing steps include the removal of bad quality data points using the manufacturer's software Ocean Contour, considering low correlation, side lobe interference and high amplitude spikes. These data have been used by Perez et al.(2021) to calculate turbulent kinetic energy (TKE), turbulence intensity (TI), Reynolds stresses, integral length scales, TKE dissipation and production rates as well as to discuss wave-turbulence interaction and the application of decomposition methods. In the dataset collected in Banks Strait, velocity fluctuation enhancements caused by wave orbital velocities were mitigated using the Synchrosqueezing Wavelet Transform (SWT) decomposition method. Turbulence estimates were organized by month and are revealed in the post-processed data files. Here we provide raw, processed and post-processed data files, which were made publicly available through the University of Queensland UQ eSpace repository. These datasets may be reused to further advance the understanding of turbulence and its impacts on tidal turbine performance as well as to help establish international guidelines for turbulence measurements in tidal energy site assessments.