Anaerobic lagoons are natural wastewater treatment systems suitable for swine farms in small communities due to its low operational and building costs, as well as for the environmental sustainability that these technologies enable. The local weather is one of the factors which greatly influences the efficiency of the organic matter degradation within anaerobic lagoons, since microbial growth is closely related to temperature. In this manuscript, we propose a mathematical model which involves the two-dimensional Stokes, advection–diffusion-reaction and heat transfer equations for an unstirred fluid flow. Furthermore, the Anaerobic Digestion Model No1 (ADM1), developed by the International Water Association (IWA), has been implemented in the model. The partial differential equations resulting from the model, which involve a large number of state variables that change according to the position and the time, are solved through the use of the Finite Element Method. The results of the simulations indicated that the methodology is capable of predicting reasonably well the steady-state of the concentrations for all processes that take place in the anaerobic digestion and for each one of the variables considered; cells, organic matter, nutrients, etc. In view of the results, it can be concluded that the model has significant potential for the design and the study of anaerobic cells’ behaviour within free flow systems.