In this paper the Bias Variance Search Algorithm is proposed as an algorithm to optimize a candidate set of initial parameters for an Extended Kalman filter (EKF). The search algorithm operates on a Bias Variance Equilibrium Point criterion to determine how to set the initial parameters. The candidate set is then used by the EKF to estimate state parameters to fit a triply modulated cosine function to time series of the first two spectral bands of the MODerate-resolution Imaging Spectroradiometer (MODIS) land product. The state parameters are then used for land cover classification. The results of the search algorithm was tested on classifying land cover in the Limpopo province, South Africa. An improvement in land cover classification was observed when the method was compared to a robust regression method.