High-frequency velocimeters used for flow measurements during laboratory experiments allow the user to select the range for several operation parameters to set up the instrument for optimal velocity measurement. The discrepancies between velocity measurements collected with different instrument configurations can be significant, depending on the flume bed configuration and boundary conditions. The aim of this paper is to quantify the differences in flow velocity profiles measured with Acoustic Doppler Velocimeter Profilers (ADVPs) configured using a combination of profiling parameters: Ping Algorithm (PA), Transmit Pulse Size (TPS), and Cell Size (CS). Whereas in Part I of this research, the goal was to identify the optimal probe configuration for downstream measurement of the complex hydraulic structure (pier protected with riprap) based on a match of the flow rate with measurements from other instruments, in this paper, effect of distinct probe configuration on velocity profile and turbulent kinetic energy (TKE) is demonstrated. Differences between ADVPs’ configurations were analyzed through sensitivity analysis with the intention to calculate and compare any discrepancies in the velocity measurements for all the three measured velocity components: streamwise u, spanwise v and vertical w collected on two characteristic flume cross- sections. The results show that each parameter change has a significant effect on the measured values of each velocity component when compared to the Target Configuration (TC). The largest root- mean-square-error (RMSE) is observed when TPS is changed, followed by CS and PA. Absolute RMSE calculated for TPS change from 4 mm to 1 mm is, on average, 6.30 cm/s, 0.90 cm/s, and 0.82 cm/s for velocity components u, v and w, respectively. Absolute RMSE calculated for CS change from 1 mm to 4 mm is, on average, 4.49 cm/s, 0.88 cm/s, and 0.71 cm/s for velocity components u, v and w, respectively. Absolute RMSE calculated for PA change from Adaptive to Max interval is, on average, 4.04 cm/s, 0.63 cm/s, and 0.68 cm/s for velocity components u, v and w, respectively. For a change in all parameters, RMSE is greater for the cross-section downstream of the pier than for the approach cross-section: on average, 90%, 57% and 54% for a change in the PA, TPS, and CS, respectively.