The acoustic communications are extremely challenging in underwater environments due to harsh conditions of this kind of nature. That medium's harshness affects the transmission reliability which in turn crucially requires an adoption of robust channel codes based on cooperative approaches to attain a more reliable data communication. This study proposes a cooperative communication system based on a protograph low-density parity check (P-LDPC) code. The system is elaborated in an Internet of underwater things (IoUT) scenario in which a relay node is acting as a helper that provides side information to destination. Compression and channel coding are offered by the system to cope with requirements of IoT in terms of reliable communication and compressed data between nodes. Furthermore, an algorithm for joint source channel coding is presented based on a modified version of offset min-sum. Moreover, layered decoding is Implemented in order to minimize number of iterations for the P-LDPC code. The results prove that proposed design can achieve a bit error rate (BER) of 5 × 10−6 at signal to noise ratio SNR = 8 dB for a coding rate of 1/3 and block length of 1500 bits. In addition, the proposed system shows a coding gain of 3.6 dB when compared with a non cooperative (no relay) approach. Besides, the proposed cooperative design can offer reduced computations versus the non cooperative system to achieve the same BER at a fixed SNR.