Due to the proliferation of underwater vehicles and sensors, underwater wireless optical communication (UWOC) is a key enabler for ocean exploration with a strong reliance on short-range bandwidth-intensive communications. A stable optical link is of primary importance for UWOC. A compact, low-power, and low-cost acquisition, pointing, and tracking (APT) system is proposed and experimentally demonstrated to realign the optical link within 0.04 s, even when the UWOC transmitter and receiver are in relative motion. The system successfully achieves rapid auto-alignment through a 4 m tap water channel with a relatively large number of bubbles. Furthermore, the required minimum illumination value is measured to be as low as 7.1 lx, implying that the proposed APT scheme is robust to dim underwater environments. Meanwhile, mobility experiments are performed to verify the performance of the APT system. The proposed system can rapidly and automatically align moving targets in complex and unstable underwater environments, which can potentially boost the practical applications of UWOC.