The presented research addresses a problem occurring in a biogas plant, which we know plays an important role in sustainable development. The sludge deposited on the walls of the digester’s heat exchanger impairs heat transfer to the substrate. It leads to a temperature drop inside the biogas plant and threatens its correct operation. The thickness of the sludge layer cannot be directly measured when the plant is operating. Therefore, the aim of this work was to develop and then validate a method for estimating, based on the operating parameters of the exchanger, the thickness of the sludge layer and to give theoretical foundations for designing an automatic sludge monitoring system. Two mathematical models (and methods) were developed: one- and two-dimensional. The former model was solved analytically while the latter by the Trefftz method. The numerical results from these two approaches showed very good agreement with each other and with the actual measurement taken directly after removing the substrate from the fermentation chamber. According to the calculation results, the growth of the sludge layer was linear with time, and its rate was 0.0064 mm per day. Finally, a schematic diagram of an intended sludge monitoring system was proposed. It could optimize biogas plant operation and thus become a step towards more sustainable energy production.