This paper presents the application of the Discrete Linear Quadratic Control (DLQC) method for a parameter optimization problem in a marine ecosystem model. The ecosystem model simulates the distribution of nitrogen, phytoplankton, zooplankton and detritus in a water column with temperature and turbulent diffusivity profiles taken from a three-dimensional ocean circulation model. We present the linearization method which is based on the available observations. The linearization is necessary to apply the DLQC method on the nonlinear system of state equations. We show the form of the linearized time-variant problems and the resulting two algebraic Riccati Equations. By using the DLQC method, we are able to introduce temporally varying periodic model parameters and to significantly improve – compared to the use of constant parameters – the fit of the model output to given observational data.