The problem of estimating multiple time delays in the presence of colored noise is considered in this paper. This problem is first converted to a frequency estimation problem by using the discrete Fourier transform. Then, sample lagged covariance matrices of the resulting signal are computed and studied in terms of their eigen-structure. These matrices are shown to be effective in extracting bases for the signal and noise subspace. MUSIC and Pencil-based frequency estimators are then derived using these subspaces. The effectiveness of the method is demonstrated on simulated backscatter which involves estimation of multiple specular components of the acoustic backscattered return from an underwater target.