This paper presents an optimal control applied to water flow using the first and second order adjoint equations. The gradient of the performance function with respect to control variables is analytically obtained by the first order adjoint equation. It is not necessary to compute the Hessian matrix directly using the second order adjoint equation. Two numerical studies have been performed to show the adaptability of the present method. The performance of the second order adjoint method is compared with that of the weighted gradient method, Broyden -Fletcher -Goldfarb-Shanno method and Lanczos method. The precise forms of the adjoint equations and the gradient to use for the minimisation algorithm are derived. The computation by the Lanczos method is shown as superior to those of the other methods discussed in this paper. The message passing interface library is used for the communication of parallel computing.