The dynamic and resource constrained nature of Wireless Sensor Networks (WSNs) require that the time synchronization protocol is highly fault tolerant whilst minimizing communication overhead for energy-efficiency. In current tree-based WSN synchronization protocols, the tree fault tolerance is not considered at all or incurs a significant messaging overhead. In this paper, we present a robust Synchronization TREE construction and maintenance protocol (S-TREE). It can handle failed nodes and communication links, and intermittent connectivity. It is integrated to the neighbor discovery to minimize communication overhead. The S-TREE protocol minimizes the accumulated synchronization error of any given neighbor clock estimation technique by using minimum hop paths to the reference node. The protocol performance is analyzed mathematically. For an example scenario of 1000 nodes S-TREE reduces communication overhead to 6% in tree construction and to 10% in remote clock estimation compared to flooding which is commonly used in related protocols.