The propagation speed of an acoustic signal is much slower than the speed of a terrestrial radio signal due to the physical characteristics of an underwater acoustic channel. This large delay can impact the throughput of the channel. There is a very high delay variance which presents unique challenges to the designs of efficient protocols. The inconsistent delay renders many traditional communication protocols insufficient since they rely on accurate estimations of the round trip time (RTT) between two communication nodes. Underwater acoustic channels are inherently unreliable with connection interruptions. In this paper we present a unique approach to develop a prediction based delay-tolerant protocol (PBDTP) to address these problems. The PBDTP protocol can tolerate long delays, inconsistent delays and connection disruptions by predicating a value for a sensor node if its data were not received at the sink node instead of having the sensor node retransmit its data. The PBDTP can reduces data traffic over the networks and uses the network resource more efficiently.