Modern underwater robotic systems require a reliable data transmission mechanism capable of accounting for the limitations of the hydroacoustic communication channel, such as high latency, low bandwidth, and the likelihood of bit errors. Existing solutions based on string-format data exchange are constrained in their ability to handle large volumes of information, reducing the efficiency of coordinated operations among underwater vehicles. This study proposes a file transfer protocol specifically adapted for hydroacoustic networks. The protocol incorporates segmentation mechanism, retransmission of lost packets, and reliable data delivery. A theoretical framework for its implementation is presented, along with a software framework for simulation and numerical results analyzing its efficiency. The developed protocol can be integrated into hydroacoustic modems from various manufacturers and used for exchanging diverse data in file format within underwater robotic systems.