Acquisition of the code timing in DS/SS systems is addressed for time-varying frequency-selective underwater acoustic channels. Acquisition algorithm based on adaptive channel estimation and filtering is proposed. The algorithm employs feedback of pre-cursor and post-cursor inter-chip interference to provide a channel estimate from which the code timing is acquired. The channel estimate is also used to filter the signal prior to making the acquisition decision. Channel estimation/filtering procedure eliminates the need for explicit equalization, and enables a computationally efficient implementation. Simulation results show excellent performance in low-SNR regime, as well as in the presence of multiple-access interference and fast fading.