Research in underwater communication is rapidly becoming attractive due to its various modern applications. An efficient mechanism to secure such communication is via physical layer security. In this paper, we propose a novel physical layer authentication (PLA) mechanism in underwater acoustic communication networks where we exploit the position/location of the transmitter nodes to achieve authentication. We perform transmitter position estimation from the received signals at reference nodes deployed at fixed positions in a predefined underwater region. We use time of arrival (ToA) estimation and derive the distribution of inherent uncertainty in the estimation. Next, we perform binary hypothesis testing on the estimated position to decide whether the transmitter node is legitimate or malicious. We then provide closed-form expressions of false alarm rate and missed detection rate resulted from binary hypothesis testing. We validate our proposal via simulation results, which demonstrate errors’ behavior against the link quality, malicious node location, and receiver operating characteristic (ROC) curves. We also compare our results with the performance of previously proposed fingerprint mechanisms for PLA in underwater acoustic communication networks, for which we show a clear advantage of using the position as a fingerprint in PLA.