To overcome the performance limitation of multipath time-delay estimation posed by underwater acoustic sinusoidal signals, an approach incorporating the frequency-domain weighting of the highly oscillatory Nonlinear Least Squares (NLS) cost function with the evolu- tionary optimization was proposed to facilitate the accurate estimation of the multipath timedelay of sinusoidal signals. In the described method, the number of the effective multipath signals, which is included into the parameter model as well as the multipath time-delay and amplitude factor, can be estimated simultaneously thus avoiding the requirement of additional computation. The experimental results performed with numerical simulation and sea-trial data are provided, demonstrating the effectiveness and precision enhancement of the proposed algorithm.