In this paper, a Universal Underwater Software Defined Modem (UniSDM) architecture is proposed that may operate in different modes (acoustic, magnetic induction, optical and RF), in order to utilize the advantages of each mode and accordingly satisfy the requirements of many latest use cases in underwater communication systems. A detailed description of the novel UniSDM architecture is presented first.The novelty of this architecture is its flexibility, i.e., allowing the designers to produce a device that may include any type of modes operating seamlessly and jointly by exchanging data, control and synchronization. Many challenges, including high system costs and coordination between different modes, are addressed in the paper. Moreover, numerical evaluation is conducted to assess the performance of the proposed UniSDM architecture. Finally, the performance evaluation shows that the utilization of the UniSDM allows to decrease the transmission latency and improve the energy efficiency, while maintaining high reliability and robustness in underwater communication systems.