In this paper, a receiver architecture exploiting the clustered sparsity of deep-sea channels via multipath cluster alignment (MCA) is developed for single-element high-rate communication. To accommodate the uncertainties of multipath structure, spread, and time variation associated with single-receiving-element deep-sea acoustic channels, the proposed receiver uses an MCA pre-equalizer to exploit clustered multipath sparsity in large-delay-spread deep-sea acoustic channels, followed by a post-equalizer to address residual inter-symbol interference. After obtaining the multipath clusters (MCs) structure, each MC is aligned along time delay to perform MCA joint equalization. This process is equivalent to decomposing the large delay spread deep-sea acoustic channel into multiple short sub-channels for joint equalization. Subsequently, the output of the MCA pre-equalizer enters a channel estimation-based turbo equalizer (CE-TEQ) to suppress residual ISI. The MCA pre-equalizer combines multiple MCs to generate a shortened and time-variation-suppressed equivalent channel, which is advantageous for the subsequent single-channel CE-TEQ to estimate this equivalent channel to yield performance enhancement via a low-complexity turbo equalizer. Simulations and deep-sea experimental results demonstrate that the proposed receiver outperforms traditional receivers. Field trials indicate that error-free communication was achieved with a maximum effective data rate of 5019.6 bps over a distance of 20 km using a single receiving element.