As threats in the maritime domain diversify, securing data transmission becomes critical for underwater wireless networks designed for the surveillance of critical infrastructure and maritime border protection. This has sparked interest in underwater Quantum Key Distribution (QKD). In this paper, we present a real-time implementation of an underwater QKD system based on the BB84 protocol. The QKD unit is built on a hybrid computation system consisting of an FPGA and an on-board computer (OBC) interfaced with optical front-ends. A real-time photon counting module has been implemented on FPGA. The transmitter and receiver units are powered with external UPS and all system parameters can be monitored from the connected computers. The system is also equipped with a visible laser and an alignment indicator to validate successful manual alignment.