In this paper, a joint synchronization and Doppler scaling factor estimation algorithm has been proposed for underwater acoustic communications. The training sequence, which consists of two Zadoff-Chu (ZC) sequences being conjugate with each other, is utilized to synchronize and estimate Doppler scaling factor, time delay and carrier frequency offsets (CFOs). ZC sequences are well designed to show high robustness with the presence of CFOs. In the receiver, a two-dimensional cross-correlation and two auto-correlation operations can accomplish Doppler scaling factor estimation, propagation delay estimation and CFO estimation. Simulation results prove the proposed algorithm is effective for underwater acoustic communication systems.