As the water supply becomes more and more scare, other water use sectors as municipal and industrial turn to agriculture for water reallocation. Take Chia-Nan Irrigation Association as an example, the held water rights are twice as much as the planned annual irrigation demand and there still a water shortage in the command area. This paper is to study how to check the current agricultural water rights, and the discrepancy between certified water rights and actual water diversion so as to eliminate the issue of over-certified water rights.