The on‐line monitoring of water quality is of crucial interest. Control charts are well suited to perform this monitoring. However, these statistical methods need to be adapted to the particularity of the environmental data studies. In this paper, new control charts are developed to treat the case of a French river for which the parameter of interest, the Dissolved Oxygen Concentration (DOC), is characterized by a non‐stationary and seasonal time evolution. The principle is to construct a test statistic, not directly based on the variable of interest, but rather on its seasonal regularity when the system is under control. The methods are studied through numerical simulation and is applied on real data. The ability of the control chart to be used as a classifier in a retrospective way is also studied. Copyright © 2016 John Wiley & Sons, Ltd.