Research challenges have focused on underwater acoustic sensor networks characterized by long propagation delay, narrow bandwidth, and frequently disconnected interruption, among others, which can be viewed as delay/disruption tolerant networks (DTNs). However, limited research has been conducted on goodput performance considering the total data packets transmitted in the channel, which is referred to as the remove redundant goodput (RRG) performance of underwater DTN sensor networks. In this paper, we propose a transport layer protocol, called optimal retransmission timeout (RTO) interval stop-and-wait transmission (ORIT), used in underwater DTN sensor networks. In most general transport layer protocols, the RTO timer is set to longer than the RTT to avoid pseudo-retransmissions. However, great network latency could be introduced by applying such a mechanism in underwater communication networks. In ORIT, we propose an RTO optimization algorithm to maximize the RRG performance of the network by reducing the RTO timer. Meanwhile, we adopt the interval stop-and-wait transmission mechanism to avoid data pseudo-retransmissions caused by setting the RTO timer shorter than the RTT in narrow acoustic channels. Through adopting the RTO timer, the ORIT can achieve the best RRG performance under an RTO timer, which we call the optimal RTO timer. We compare the ORIT with other transport layer protocols in the DTN network. The results show that the ORIT with the optimal RTO timer can shorten the long propagation delay and effectively increase the data delivery rate in the underwater DTN sensor networks.