Abstract. According to a reduction in available water resources such as rainfall and groundwater; today, the supply of drinking water has become one of the main problems of the worldwide countries. Seawater desalination methods are one of the alternatives to deal with this problem, among which the employment of distillation units by means of solar radiation can be a suitable and cost effective alternative. Multi-effect distillation is one of the thermal desalination systems that have received great attention today due to energy efficiency and high performance. In this paper, a PDE and non-linear model from MED desalination systems has been initially presented. To understand how these systems work, one is required to have a sound understanding of the behavior of the system variables while access to the exact value of these variables is not possible due to the presence of noise in the system model. Thus, due to the nonlinearity of the model of the system, extended Kalman filter (EKF) was proposed to provide a desired approximation of the system variables in addition to reducing the noise in the system. The simulations conducted in MATLAB software show that the employed algorithm has been largely successful.