Acoustic Doppler current profiler (ADCP) uses acoustic energy directed along narrow beams for current measurement. In conventional method, the quantity of sampling affects the precision of fast Fourier transform (FFT) algorithm, and the algorithm needs a large amount of data to process. A novel frequency estimator,enhanced least mean square (ELMS) algorithm for a single complex sinusoid in complex white Gaussian noise, is proposed in ADCP system. As sampling frequency equals 120 krad/s and the sampling number equals 240, the minimum resolving is 0.5 krad/s. All variances keep 11.11%. ELMS algorithm needs less data than FFT. And the robust algorithm can estimate the spectrum true value to 99.9% when the signal to noise ratio (SNR) is equal to 0 dB. Experiments prove that the estimation values will diverge much from the ideal when SNR is less than -6 dB.