This thesis presents the design and implementation of an underwater network communication protocol. The goal is to enable several autonomous underwater vehicles (AUVs) to form a communication network and to exchange information during at-sea missions. The focus of this work is on the upper layers of the protocol: Network and Transport layers. Routing is a critical issue since all the nodes forming the network are moving. A study and comparison of existing routing algorithms is presented. Two routing algorithms have been chosen and implemented in the network layer of the protocol: Flooding and Destination Sequence Distance Vector Routing. The protocol has been tested on several types of simulated missions. An analysis of the results is proposed for each mission.