For the first time a mobile underwater Full Tensor Magnetic Gradiometer (FTMG) system based on low-Tc Superconducting Quantum Interference Devices (SQUIDs) has been deployed in order to scan the seafloor for magnetized targets. The application is mainly focused on waste deposits and unexploded ordnance (UXO), but could also include shallow geological features as well as archaeological remainders. The main methods for detection and localisation of underwater UXO and waste deposits are side sonar scanning and magnetic mapping. While modern sonar scanners can achieve a very high spatial resolution and long detection range, they still have problems detecting targets under cover – for magnetic sensors a layer of non-magnetic sand or ooze does not have an effect on the signal apart from an increased distance. This paper discusses the setup of the mobile underwater FTMG SQUID system, its challenges and main performance features. It also illustrates its detection and localization capabilities in tests on known magnetic targets.