A current velocity measurement radar estimates Doppler frequencies to extract the corresponding surface velocity information. Therefore, it is required to maintain the high degree of reliability and accuracy of Doppler frequency estimates. However, Doppler spectra of water surface return echoes can have very widely varying shapes according to measurement environments and weather conditions. Therefore, serious problems may arise in maintaining the reliability and accuracy of conventional velocity estimating algorithm in a radar sensor. Therefore, in this paper, a newly suggested algorithm is proposed for improvement using estimation of peak Doppler frequencies. The proposed method shows that the more accurate velocity measurement can be possible comparing with the conventional one.