In automated container terminals, situations occur where quay cranes, stacking cranes, and automated guided vehicles (AGVs), directly or indirectly request each other to start a specific process. Hence, all of the affected resources are blocked, possibly leading to the complete deadlock of individual cranes or AGVs. Particularly, AGVs are liable to deadlocks because they always need a secondary resource, either a quay crane or a stacking crane, to perform the pick-up and drop-off operations. Because usually no buffering of containers takes place at the interfaces between AGVs and cranes, the consequences of deadlocks are rather severe. Two different methods for the detection of deadlocks are presented. One is based on a matrix representation of the terminal system. The other directly traces the requests for the individual resources. To resolve deadlock situations arising in an automated container terminal, three different procedures are proposed. These procedures aim to modify the sequence of handling operations or to assign them to alternative resources so that conflicts between concurrent processes are resolved. The suitability of the concept is demonstrated in an extensive simulation study.