Marine communication has attracted widespread attention in the wake of global warming and national defense awareness in recent years, where acoustic systems enabling smooth underwater communication have become a popular research topic. In this study, we proposed an underwater communication system equipped with modulators and demodulators (modems). Specifically, the wireless communication software GNU’s Not Unix Radio (GNU Radio) was adopted to develop communication formats and architectures applied to a Raspberry Pi computer, on which we developed a communication format available for signal synchronization to increase system robustness against underwater channel interferences. We also developed hardware and software modems for the system. The hardware device was developed using the XR2206 function generator and XR2211 equipment for frequency-shift keying (FSK)-based modulation and demodulation, respectively. The software FSK modem was developed using GNU Radio. To increase the robustness of the transmitted data, we added a cyclic redundancy check through the Async CRC32 block, after which the power distribution unit (PDU) to the Tagged Stream block placed a tag to the start of data combined with effective loads and CRC32, facilitating the attachment of header generators. Four experiments with different underwater scenarios were then conducted to verify the proposed system. The hardware modem had a 0 bit error rate (BER) during experiments implemented in a laboratory sink, a 20-m-long indoor swimming pool, and a 50-m-long outdoor swimming pool, compared with BERs of 2.8 × 10−3 and 6.6 × 10−3 during the breeding water tank experiment under transmission rates of 1 and 2 kbps, respectively. Similarly, the software modem delivered 0-BER performance in the laboratory sink as well as in the indoor and outdoor swimming pools, with its BERs being 2.3 × 10−4 and 2.98 × 10−4 under 1 and 2 kbps transmission rates, respectively. The proposed system comprises preambles, headers, and effective load communication formats for signal protection. In particular, its directional ultrasonic cylindrical piezoelectric transducer can mitigate multipath effects and interferences, thereby enhancing system robustness.