Studies have reported the incorporation of microorganisms into cement to promote the formation of calcium carbonate in cracks of concrete, a process known as biomineralization. The paper aims to improve the process of the cascade system for biomineralization in cement by identifying the best hydrodynamic conditions in a reaction cell in order to increase the useful life of concrete structures and, therefore, bring energy and environmental benefits. Two central composite rotatable designs were used to establish the positioning of the air inlet and outlet in the lateral or upper region of the geometry of the reaction cell. The geometries of the reaction cell were constructed in SOLIDWORKS®, and computational fluid dynamics was performed using the Flow Simulation tool of the same software. The results were submitted to statistical analysis. The best combination of meshes for the simulation was global mesh 4 and local mesh 5. The statistical analysis applied to gas velocity and pressure revealed that air flow rate was the factor with the greatest sensitivity, with R2 values up to 99.9%. The geometry with the air outlet and inlet in the lateral region was considered to be the best option.