An estimation procedure for suspended sediment concentrations based on the intensity of backscattered sound of acoustic Doppler current profilers (ADCP) is introduced in this paper. Based on detailed moving and fixed boat ADCP measurements with concurrent sediment sampling, we have successfully calibrated the estimation method for a reach of River Danube in Hungary, characterized by significant suspended sediment transport. The effect of measurement uncertainty and various data filtering on sediment load determination is also analyzed and quantified. Some of the physical model parameters describing the propagation of sound in water are estimated based on known empirical formulas, while other parameters are derived from measured. Regression analysis is used to obtain a relationship between the intensity of backscattered sound and sediment concentrations. The empirical relationship has been then used to estimate the suspended sediment concentrations from the ADCP data collected in fixed and moving boat measurement operation mode, along verticals and path-lines, respectively. We show that while some measurement uncertainty is inherent to the acoustic Doppler principle, it is further enhanced by the complexity of the near-bottom sediment-laden flow. This uncertainty has then a significant effect on the local sediment load estimation. In turn, reasonable smoothing of raw velocity and backscatter intensity data shows insignificant impact on cross-sectional sediment load estimation.