The paper presents a methodology for the Algorithmic Process Synthesis of activated sludge processes. The difficulty for the engineers to carry out the process synthesis comes from the complexity and the high non-linear behaviour of these biological processes. The paper proposes the way to carry out the algorithmic synthesis for this particular type of complex processes. The proposed method requires the development of a network of interconnected units, the process superstructure, which contains lots of alternative process flowsheets, and the mathematical model of such superstructure. From these two elements, the optimisation model must be obtained. This optimisation model contains a mixed set of binary and continuous variable and the solution of the corresponding optimisation problem provides the optimal values for the units size, the best way to connect them and a working point for certain pre-specified conditions. In the work presented in this paper, the cost function includes multiple objectives associated to the building and the operation costs. Due to the non-linearity of the model for activated sludge processes, the problem is classified as Mixed-Integer Non-linear Programming problem (MINLP). In this work we present the whole procedure taking as illustrative example of Process Synthesis the mentioned above biotechnological process.