This article presents the results of natural carrying capacity of ponding irrigation system in Taoyuan agricultural zone, Taiwan. Both the systematic water quality and the ponding effects were examined. The ponding irrigation system included a flow channel and storage ponds. The data showed that most water characteristics deteriorated gradually from upper- to down-stream in the flow channel and the flow channel was not attributed to any self-purification in agricultural returning water practically. On the other hand, the results of storage ponds indicated that they can provide a natural treatment (i.e., the outlet water quality of the ponds is more desirable than that of the inlet). Consequently, the ponding irrigation system offers the natural self-purification in ponds to reuse and recycle the returning agricultural wastewater and to extend the irrigation capacity and efficiency.