The unique characteristics of the Underwater Acoustic Communication (UWAC) channel cause the UWAC systems to be very vulnerable to the malicious attacks. So, the bionic-based UWAC has been used due to its good covert performance, and its suitable frequency and correlation properties. It may not be covert in all the underwater environments, or an adversary can detect the message anyway. Therefore, this paper aims at proposing an improved Merkle hash tree based secure scheme that can resist the current possible underwater attacks, i. e., the replay attack, the fabricated message attack, the message altering attack, and the analyst attack. The security analysis indicates that the proposed scheme is resilient to the mentioned attacks. Also, the performance evaluations show that the proposed scheme is proportional to the UWAC limitations due to its efficiency in terms of energy consumption, communication overhead, and computation cost.