[Objective] Accurately estimating the friction velocity within the backwater region of deposit body is crucial for deriving hydraulic parameters and predicting river scour and deposition. While classical friction velocity methods (e.g., the logarithmic velocity method) are well-established for uniform flows, their applicability and the associated velocity-turbulence parameter characteristics in backwater regions with non-uniform deposits remain systematically underexplored in current research. [Methods] We conducted a series of flume experiments, employing three distinct flow rates to simulate conditions ranging from low to heavy rainfall during the rainy season. A plexiglass deposit model, characterized by a 45° slope and a channel width contraction ratio of 0.5, was utilized. Three-dimensional velocities and water levels were measured at 19 cross-sections using an Acoustic Doppler Velocimeter (ADV) to systematically analyze the hydraulic characteristics of the deposit-induced backwater region. Four classical methods-the Single-point Reynolds Stress Method, Three-dimensional Turbulent Kinetic Energy Method, Vertical Turbulent Kinetic Energy Method, and Logarithmic Velocity Method were selected to estimate friction velocity, and their relationships with backwater characteristics were investigated. The Karman constant (k) and integration constant (A) were fitted based on the measured velocity distributions. Additionally, empirical coefficients D and λ were derived from turbulence intensity measurements to elucidate their influencing factors. [Results] The key findings of this study are as follows: (1) The Three-dimensional Turbulent Kinetic Energy Method and the Single-point Reynolds Stress Method proved most effective in characterizing bed friction under the influence of deposits, yielding the smallest relative deviations for the estimated mean friction velocities. Furthermore, a significant monotonic negative correlation was observed between friction velocity and the backwater parameter (h/h₀). (2) While the vertical velocity profiles within the backwater region still adhered to a logarithmic distribution, the mean Karman constant (k) fitted across the entire water depth was lower than the conventionally recommended value of 0.4. Consequently, the integration constant (A) is proposed to be revised to 7.5-9.5 to better align with engineering requirements. (3) The empirical coefficient D for turbulence intensity was found to be jointly influenced by both flow rate and the friction velocity model, exhibiting a stable mean ratio of D_u∶D_v∶D_w=1.41∶1.00∶0.40. In contrast, λ was solely driven by flow rate. The observed decaying trend of vertical, longitudinal, and transverse turbulence intensities with increasing water depth further corroborated the reliability of the friction velocity estimations. [Conclusion] This research successfully identified the optimal method for estimating friction velocity in backwater regions characterized by non-uniform deposits and refined the empirical values of velocity-turbulence parameters. The findings offer crucial experimental evidence for advanced hydraulic modeling, flood control engineering design, and river management strategies in mountainous river sections affected by deposits. Furthermore, this study holds significant implications for river restoration efforts following earthquake-induced secondary geological hazards.