In order to use the optimal control techniques in the models of geophysical flow circulation and other research fields, an application with the control of initial and boundary conditions to Brugers equation is described. In a general case, the continuous problem and corresponding discrete form are formulated, in which the so called adjoint variable is introduced and then the adjoint equation is derived. The impacts on the optimal control for the error with various frequencies in initial control are considered. The effects and ability of this optimal control method are analyzed, in which the observational data used are obtained by the linear interpolating in spatial grids from original observational data. This method proves to be efficient and useful.