Abstract At high temperature, the circulation of fluid in heat exchangers provides a tendency for fouling accumulation to take place on the internal surface of tubes. In brief, the deposits on heat exchanger tubes are caused by the presence of inorganic salts, of small quantities of organic materials and products of corrosion in the water. From thermophysical point of view, the deposited fouling has harmful effects on the heat exchanger efficiency. Indeed, it increases the thermal resistance which can raise the energy consumption. This study shows an experimental and a theoretical process of estimation of thermophysical properties of the fouling deposited on a section of a heat exchanger and its effects on the heat transfer efficiency. The estimation method is based on the Gauss–Newton algorithm that minimizes the ordinary least squares function comparing a measured temperature and a theoretical one. The temperature response is measured on the rear face of a bi-layer system composed of a section of a heat exchanger and the fouling deposited on during and after a finite width pulse heat flux on its front face. The theoretical temperature, that is a function of the unknown thermophysical properties of the bi-layer system, is calculated by the resolution of the one-dimensional linear inverse conduction problem, and by the use of the quadrupole formalism. The results of the estimation procedure show, on the one hand the efficiency and the stability of the optimization algorithm to estimate the thermophysical properties of the fouling. On the other hand they underline the necessity of the maintenance of fluid circulating tubes at high temperature.