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Multivariable design techniques are applied in an application to the identification and subsequent online control of an interacting network of flows feeding one of the largest water treatment works, WTW, in the North West of England. The development of a multivariable process model from data obtained directly from the plants SCADA system is described. The developed process model was then used to design a conventional diagonal multi-loop SISO controller by detuning the controllers from SISO Ziegler-Nichols settings until a multivariable stability criterion was satisfied. By controlling the flow rate to the plant and minimising flow disturbances through the WTW, the potential of Cryptosporidios, a protozoan parasite, within the water supply has been minimised. A comparison with a more advanced model based predictive control scheme is also presented.