The pond irrigation system, which was developed in the early twentieth century, is an effective rainfall harvesting method that exploits geographical features to overcome hydrologic disadvantages. The concept of the pond irrigation system is to reserve excess rainwater runoff in farm ponds that act as small reservoirs supplying water to farmlands during the drought periods. This study aimed to promote the pond irrigation systems in the Tao-Yuan area. The irrigation system model developed in this study shows how agriculture water demand in a region can be fulfilled by adjusting system dynamics of waterways such as canals, river weirs, and farm ponds. This water demands can be met in 2 ways: (1) deep-ponding irrigation and (2) adjusting the backup storage ratio of farm ponds between up- and down-stream areas. Our analytical results showed that deep-ponding irrigation could be used to effectively harvest rainfall to reduce agricultural water demands from the Shih-Men Reservoir and increase the amount of water reserved for farming purposes. Furthermore, in our model, during drought periods and/or when the reservoir water supply is inadequate, the backup water storage ratio in the downstream regions is greater than that in the upstream regions, such that water in upper ponds is reduced and the storage capacity of lower ponds is increased to store more return flow from upstream.