In order to cope with the problem of information leakage of existing secret-key agreement protocols under the environment of underwater acoustic channel (UAC), a covert secret-key agreement protocol called CSAP is proposed. In CSAP, the transmitter sends the uniformly distributed random messages to the receiver within a certain range of power constraints to ensure the reliability and the covertness of the protocol. The receiver calculates the estimated messages with Gibbs sampling according to the variance information of the underwater noise and uses the Log-Likelihood Ratio (LLR) test to extract the secret-key so as to reduce the uncertainty and the bit error rate (BER) of data transmission between two legitimate parties. The complexity of the CSAP protocol is <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${O}$ </tex-math></inline-formula> ( <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${n}$ </tex-math></inline-formula> ), where <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">${n}$ </tex-math></inline-formula> denotes the message length. The secrecy, covertness, and reliability of the CSAP protocol are proved by the information theory. The simulation results show that the CSAP protocol reduces the bit error rate (BER) by 28.88%, improves the secret-key generation rate by 25.70%, and decreases the communication cost by 11.32% on average compared to the existing protocol.