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In this paper, we propose a frequency domain adaptive estimation of Doppler shifts for multiple Doppler subpaths in direct sequence code division multiple access (DS-CDMA) systems. By modeling the doubly selective channel using a basis expansion model (BEM), the proposed expectation-maximization (EM) algorithm-based estimation method can obtain accurate information of Doppler shifts. Based on the estimated information of Doppler shifts, a FDE-based receiver architecture is developed to exploit Doppler diversity in frequency domain. Simulation results demonstrate that this receiver structure features a low computational complexity while achieving good performance compared with traditional receiver structures in DS-CDMA systems.