Constructed wetlands (CWs) are artificially constructed ecosystems for treating contaminated water through creating a mesocosm of soil, vegetation, and microorganisms [1]. Mesocosms are a controlled ecosystem that simulates a natural environment, allowing for experiments to observe the behavior and characteristics of the system under controlled conditions [2]. CWs can be engineered to promote the development of a biofilm, or a bacteria formation in a moist environment, which is responsible for the biodegradation of contamination in wastewater. However, bioclogging is a major challenge that occurs in the application of CWs due to accumulation of bacteria in areas of low flow, decreasing the permeability to wastewater and causing dead-zones to form. Dead-zones exacerbate low-velocity flow and lead to preferential flow through low-biofilm concentration regions, reducing contaminant removal efficiency. The present study implements a computational fluid dynamics (CFD) simulation in COMSOL to investigate the effect of flow behavior through a porous medium on biofilm development in a simulated mesocosm. The goal of the model is to observe the effects of the inlet fluid flow on the development of dead-zones to optimize the CWs. The mesocosm was modeled in COMSOL 6.0 as a 3D cylindrical vessel containing pea gravel as the porous medium, along with the various reactions of organic matter growth and decay. The two main processes observed are the fluid flow, modeled using Free and Porous Media flow, and the mass balances of organic matter and biomass, modeled using the Transport of Diluted Species. To simulate the bioclogging effect, the porosity and permeability of the porous medium are coupled to the concentration of biomass, along with the detachment of biomass from biofilm due to fluid flow shear stress. The model predicted non-uniform biofilm development, with areas of higher biofilm concentration resulting in lower porosity and permeability. The fluctuations in porosity throughout the geometry result in varying fluid velocity. Reduced biofilm growth is observed in high-velocity regions, while higher concentrations of biofilm can be found in areas with low velocity due to bioclogging. By varying the inlet flow rate, the behavior of biofilm development can be observed and optimized to reduce the ramifications of dead-zone formation on the efficiency of contaminant removal.