Within the last 10 years throughout south-eastern Australia, there has been a rapid expansion of modernisation efforts by irrigation companies that has included installation of automatic control structures, the so-called total channel control (TCC) technology. TCC includes supervisory control and data acquisition technology, which results in production of integrated databases utilising real time measurements of flow and water depth throughout the whole system. Pondage tests are acknowledged as the best direct method for seepage measurement and the recorded water level data from automated systems during periods of gate closure can be treated as pondage test data. This paper presents the development and operation of a new computer model that applies pondage test methodology to automated channel control data during periods of shut down in order to estimate seepage rates in different channel reaches. The Coleambally Irrigation Area (CIA) in southern New South Wales was chosen as the case study, as it is one of the first irrigation districts in the world to be automated. The methodology was tested using the TCC data of the entire CIA during the 2010–11 season and was demonstrated to be successful in identifying all pondage conditions throughout the entire network as well as estimating the seepage rates for each gauge, pondage and pool.