Sediment on the bottom of borehole forms a major part which is often responsible for reducing the bearing capacity of pile. The normal method of measuring sediment thickness by ultrasonic signal is to measure the sound time and intensity of echo signal. This paper presents a novel measurement method by estimating the ultrasonic channel. Wiener filter is applied to estimate the ultrasonic optimal channel under minimum mean square error criteria. Experiments of estimating channel based on Wiener filter have been conducted with given signals and actual ultrasonic detection echo. The influence of noise in the signal has been discussed. The results show that, during signals high SNR, the estimated channel is corresponding to the sharp changes in the actual signal and can be used to determine the sediment thickness.