Bathymetric light detection and ranging (LiDAR), which uses a laser with narrow pulse width and a high-repetition-rate, requires a real-time data acquisition system (RTDAQS) for quickly transmitting data with the characteristic of high sampling rates, high resolution and high accuracy. However, none of the RTDAQS in the world has reached these requirements. For this reason, this paper presents a RTDAQS with high speed SerDes data transfer technology based on the architecture of ADC+FPGA+ZYNQ. This RTDAQS consists of acquisition board and storage board. The acquisition board integrates high-speed analog-to-digital converter (ADC) acquisition module, Input/Output (I/O) control module, data transmission module, and Field Programmable Gate Array (FPGA) chip module. The storage board integrates FPGA Mezzanine Card (FMC) interface, solid state and ZYNQ chips. The corresponding software includes configuration for high-speed ADC acquisition module, I/O control module, data transmission module, and FMC interface module. The RTDAQS, which is embedded in the LiDAR with laser pulses width of 2.5ns ± 0.2ns and frequency of 500 Hz, has been verified by the experiments in indoor sink, outdoor pond, river, reservoir, Beihai Bay of the Pacific Ocean. The experimental results and comparison experiments demonstrate that the presented RTDAQS can reach a sampling rate of 2 GSPS and a sampling resolution of 14 bits and a sampling accuracy of 6 LSB with an acquisition error within 0.1 m, which meet the demands of high sampling rate with high accuracy data acquisition and quick data transmission in practice and can be applied to various devices.