The ENDURUNS project is a European Research project of the Horizon 2020 framework, which has as its main objective to achieve the optimum and intelligent use of green hydrogen energy for long-term ocean surveys. The ENDURUNS system comprises an Unmanned Surface Vehicle (USV) and an Autonomous Underwater Vehicle (AUV) with gliding capability. The power pack of the USV integrates Li-ion batteries with photovoltaic panels, whilst the AUV employs Li-ion batteries and a hydrogen fuel cell. It is essential to develop a continuous monitoring ca-pability for the different systems of the vehicles. Data transmission between the devices onboard presents challenges due to the volume and structure of the different datasets. A telecommunications network has been designed to manage the operational components considered in the project. The autonomous vehicles perform measurements, providing their position and other data wirelessly. The system will generate a great volume of various signals during the survey. The Remote Control Centre needs to be interfaced with the vehicles in order to receive, manage and store the acquired data. An Underwater Internet of Things (IoT) platform is designed to establish efficient and smart data management. This study presents an exhaustive survey to analyse the telecommunication systems employed in the autonomous vehicles, including the back-end, user interface and mobile units. This paper presents the novel design of the hardware and software structure of the ENDURUNS project with regard to the literature, where its components and their in-terconnection layers are detailed, which is a novel scientific and technological approach for autonomous seabed surveying in deep oceans or in coastal areas.