The purpose of this study is to undertake the analysis of underwater detection and tracking using the Doppler phase-shift effects to enhance the detection capability. The fundamental principle is owing to the fact that the M-sequence may result in a better distinction to the echo returning from a moving target than the traditional LFM signal, in that the matched filter using M-sequence may need to estimate and compensate the doppler shift due to the moving target. The experiments were carried out in two harbors: True Love Pier of Kaohsiung Harbor (TLPKH) and Woods Hole Hrabor (WHH). The TLPKH is an inner harbor, with sediment being mud, while the WHH is an open types, suitable for target detection. The results from WHH experiment has shown that when the results from M-sequence and traditional LFM signal were compared, the M-sequence yields much better capability both in detection and estimation of the speed of the moving target along the beam axis. However, the signals from TLPKH were too weak for analysis, therefore, the data from TLPKH were used to analyze the environmental noise, transmission loss, which were combined with estimated values for sonar parameters to conduct the sonar performance analysis in an harborenvironment.