Microbial-enhanced oil recovery (MEOR) has been considered as a promising technique to further increase oil recovery from petroleum reservoirs. Although the potential benefits of MEOR applications are considerable, engineering of oil recovery via the manipulation of microbial metabolism still remains an unproven concept rather than a highly desirable reality. One of the main reasons is that there are few tools appropriate to quantify the multiple metabolic and physical processes involved in the oil recovery. This study seeks to address the lack of tools by presenting a computational model for simulating coupled processes in MEOR systems with two mobile, immiscible fluids. The primary goal of MEOR is to reduce the residual oil saturation. The residual saturation changes as a function of the capillary number that defines the relative effect of viscous forces versus surface tension acting across an interface between oil and water. In all previous MEOR studies, no explicit relations between residual oil saturation and capillary number were incorporated into theoretical models although this concept is often used in commercial reservoir simulators to simulate interfacial tension (IFT) modification. In this study, a functional relation between residual oil saturation and capillary number is achieved through solution of a coupled biological (B) and hydrogeological (H) finite element model. The BH model is quite sophisticated and difficult to solve numerically, however, presentation of the model results is simple and straightforward. A robust implicit method that incorporates a number of cross couplings between the BH processes is developed to solve the BH model. The model results are presented as a simple relation between the residual oil saturation and the capillary number and are compared to data from a well-documented core-flooding experiment. The model is applied to perform parametric studies for different microbial flooding scenarios. The BH model incorporates a description of the evolution of porosity and permeability that depends on the combined effects of the interactions between the BH processes. The model is used to predict the enhancement of oil recovery in a simple homogeneous test case. The model results demonstrate that MEOR could enhance the oil recovery significantly if a larger capillary number (between 10(-5) and 10(-1)) is achievable.