Acoustic Doppler Current Profilers (ADCP), designed for measuring velocity profiles, are widely used for the estimation of suspended sediment concentration from acoustic backscatter strength, but its application to estuarine environments requires further refinement. In this study, we examined the inversion capability of two ADCPs with 600 and 1200 kHz in three Korean estuaries: the supra-macrotidal Han River Estuary (HRE), microtidal Nakdong River Estuary (NRE), and anthropogenically altered macrotidal Yeongsan River Estuary (YRE). In particular, we examined the relative importance of the sound attenuations due to water (αw) and sediment (αs) in response to sediment characteristics (size and concentration) as well as changing salinity and temperature. The inverted concentration was compared with reference concentrations obtained either from water samples or Optical Backscatter Sensors. In NRE and YRE, where suspended sediment concentrations were less than 0.2 g/l, the acoustic inversion performed poorly only with αs (r = 0.20 and 0.38 for NRE and YRE, respectively), but well with αw (r = 0.66 and 0.42 for NRE and YRE, respectively). Thus, it is important to accurately constrain αw in low-concentration estuarine environments. However, we did not find that the varying αw performed considerably better than the constant αw. On the other hand, the acoustic inversion was poorest at HRE regardless of αw and αs (r = 0.71 and mean relative error = 45%). The large discrepancy appears to result from the poorly constrained, spatially and temporally varying sediment characteristics (grain size, density and concentration) due to non-local sediment transport in the macrotidal HRE.