For modeling of biological processes that operate close to the dynamic equilibrium (eg. anaerobic processes), it is critical to prevent the prediction of positive reaction rates when the reaction has already reached dynamic equilibrium. Traditional Michaelis-Menten based models were found to violate the laws of thermodynamics as they predicted positive reaction rates for reactions that were endergonic due to high endproduct concentrations. The inclusion of empirical “product inhibition factors” as suggested by previous work could not prevent this problem. This paper compares the predictions of the Michaelis-Menten Model (with and without product inhibition factors) and the Equilibrium Based Model (which has a thermodynamic term introduced into its rate equation) with experimental results of reactions in anaerobic bacterial environments. In contrast to the Michaelis-Menten based models that used traditional inhibition factors, the Equilibrium Based Model correctly predicted the nature and the degree of inhibition due to endproduct accumulation. Moreover, this model also correctly predicted when reaction rates must be zero due to the free energy change of the conversion reaction being zero. With these added advantages, the Equilibrium Based Model thus seemed to provide a scientifically correct and more realistic basis for a variety of models that describe anaerobic biosystems.