In this paper, we discuss the performance of different network protocols for RACUN, a European Defence Agency project with the objective of demonstrating ad hoc underwater networks for multiple purposes related to security. The RACUN network is designed for long-range communications over areas of large size, hence a very important role is played by the network protocols employed. We show that the channel realizations observed in typical scenarios and the physical layer schemes available in the project lead to significant bit error rates. Therefore, the protocols that offer some inherent form of redundancy, as in the case of flooding-based protocols, tend to yield better performance than protocols based on the exchange of signaling traffic. In support of this statement, we simulate two scenarios for the RACUN network over channel realizations that are statistically derived from real channel measurements. Our results provide insight on the advantages and drawbacks of the different packet forwarding strategies, and confirm that flooding-based approaches perform better. In addition, we prove how splitting packets into multiple fragments to match the modem's maximum service data unit significantly limits the performance