The paper presents the design of an algorithm used in control of a sequencing batch reactor (SBR) for wastewater treatment. The algorithm is used for the on-line optimization of the batch phases duration which should be applied due to the variable input wastewater. Compared to an operation with fixed times of batch phases, this kind of a control strategy improves the treatment quality and reduces energy consumption. The designed control algorithm is based on following the course of some simple indirect process variables (i.e. redox potential, dissolved oxygen concentration and pH), and automatic recognition of the characteristic patterns in their time profile. The algorithm acts on filtered on-line signals and is based on heuristic rules. The control strategy was developed and tested on a laboratory pilot plant. To facilitate the experimentation, the pilot plant was superimposed by a computer-supported experimental environment that enabled: (i) easy access to all data (on-line signals, laboratory measurements, batch parameters) needed for the design of the algorithm, (ii) the immediate application of the algorithm designed off-line in the Matlab package also in real-time control. When testing on the pilot plant, the control strategy demonstrated good agreement between the proposed completion times and actual terminations of the desired biodegradation processes.