In this paper, the processing of temporal PolSAR image series is addressed through a region-based and multi-scale data representation, the Binary Partition Tree (BPT). This structure contains useful information related to the data structure at different detail levels that may be employed for different applications. The construction of this structure ans its exploitation is addressed in this work in the context of the speckle filtering and data segmentation applications. A new region model and processing strategy are defined to tackle with the temporal dimension of the data. Finally, to illustrate the capabilities of the proposed technique, results are shown with a real RADARSAT-2 dataset.