This paper proposes an automatic method to tune a series of distant downstream PI controllers for a cascade of pools. The methodology we present could also be used for local upstream controllers, with minor changes. Examples of such systems are irrigation canals or rivers with a series of dams and hydropower plants, such as the Rhône river in France. The method is based on the Auto-Tuned Variation principle (ATV) carrying out a relay experiment. The information obtained from this experiment allows to estimate the critical gain and critical frequency of each canal pool. This information is also used to estimate the parameters of a simplified integrator-delay model of each canal pool. Finally this allows tuning PI controllers, with given gain and phase robustness margins. This relay experiment is performed for each pool of the canal, on sequence, with automatic activation of the previously tuned PI controllers, in order to tune each distant downstream controllers in series. The method is evaluated in simulation on a bench-mark canal of 5-pools in series.