The demand for transport between terminals within port areas, known as inter terminal transport (ITT), is increasing. This paper proposes a dynamic rolling horizon scheduling strategy for ITT using waterborne Autonomous Guided Vessels (waterborne AGVs). The strategy is dynamic in that it can handle the dynamically arriving ITT requests and adapt transport schedules accordingly in real time. Specifically, every certain period of time, we formulate and solve a pick-up and delivery problem considering the dynamic vessel states, waterway network topology, and ITT requests over a future time horizon. In the dynamic setting, waterborne AGVs are allowed to divert from the previously scheduled destination. Moreover, the distances between terminals are not calculated simply as the Euclidean metric but based on the complex port waterway network, which complicates the dynamic problem even more. Time windows of ITT requests, capacity constraints of waterborne AGVs and load/unload service times at terminals are also taken into account. A waterborne ITT transport network in the Port of Rotterdam is constructed. Simulation results demonstrate the effectiveness of the proposed dynamic scheduling strategy.