Based on investigating the spatially distributed input-output relationship of disinfectant residual in water distribution networks, this paper formulates the water quality control problem of multiple nodes in an adaptive optimal control framework, with special consideration on the periodic variation of parameter uncertainty and imposed bounds on the control input. The periodic parametric uncertainty, which arises due to varying consumer demands, is represented by a Fourier series with on-line parameter estimation of the unknown coefficients. A modified indirect adaptive control scheme for a single-input is studied, and then is extended to the case of multiple disinfectant boosters. A simulation example is provided to illustrate the performance of the algorithm in a real water distribution network.