An integrated approach to control of quantity and quality in water supply and distribution systems is proposed. The integrated control consists in optimising the operational cost, meeting a demand on water of desired quality and maintaining the system constraints. This constrained optimising control problem is complex due to nonlinearities, large dimension, output constraints, mixed-integer structure of the variables involved, at least two time scales in the system dynamics and an uncertainty. A sub-optimal two-level hierarchical control structure is proposed that allows incorporating the desired controller functions and yet making the synthesis of these functions possible. The algorithms for implementing the functionalities are proposed and discussed. Detail design of the lower level controller is presented and investigated. The controller performance is validated by simulation.