One of the significant problems in our society is the handling and processing of the vast amount of waste produced by households and industrial processes. Nowadays, packaging material regulations are constantly changing, which can significantly impact the quality of municipal waste, requiring the continuous development and redesign of waste processing plants. Since only a few uncertain measurements (composition, mass, etc.) are available for this task, analysing and redesigning waste processing technologies is challenging. This research aims to develop a modelling and simulation concept that can integrate all the available information and can also handle the uncertainty of the measurements. The proposed modular modelling framework can serve as a basis for designing and redesigning the technologies needed to process ever-changing municipal waste. The most important steps of the framework are as follows: identifying the typical equipment, these are the elements; building models of the elements; determining the characteristic parameters of the equipment; exploring the possible relationships between the elements. For example, the information needed to define the model parameters can be gathered from measurements, industrial experience, and expert knowledge. In many cases, the data obtained represent ranges. The stationary model framework applies efficiency factors and divides the solids into substreams based on expert knowledge. Furthermore, a modular simulator framework was developed to simulate the technological schemes with various connections. The specifications for all widely used waste industrial equipment (shredders, air separators, sieves, magnetic-, eddy current-, optical-, and ballistic separators) were used to construct the developed simulator. This simulator can open new opportunities for the design of waste sorting technological networks. The model was calibrated based on expertise gained from operating the studied technology. The changes in the material parameters can be considered, and the modular simulator can lead to flexible waste sorting technologies capable of adapting to governmental and environmental regulations changes. The main result of the work is that a methodology for designing a modular simulator, model development, and a validation method has been proposed, which provides the possibility to deal with uncertainty. All this is successfully presented through the analysis of an operating waste separation system.