The in-depth knowledge of reservoir heterogeneity is imperative for identifying the location of production and injection wells. The present study aimed at experimentally investigating the process of water flooding in the viscous oil-saturated glass micromodels, which contain layers with different permeability where the fractures were placed in different locations. Computational Fluid Dynamics (CFD) simulations of flooding were also conducted to study the impact of different water flow rates and wettability states. The results showed that the fractures, which have a deviation with the trend of maximum pressure gradient line, would widen the water path and vice versa. The performance of injection wells would increase the recovery factor by 18% if these would be located in the zones with high permeability for low flow rates of water. With changes in wettability state from water to oil wet conditions, the oil production will increase by 11%. Computational Fluid Dynamics results also indicated that an increase in the capillary number from 0.8 × 10−6 to 1.6 × 10−5, would cause the recovery factor to decrease as much as 14.34% while further increase from 1.6 × 10−5 to 2.24 × 10−5, the oil production will increase by 9.5%. Comparison between the obtained oil recoveries indicates that the maximum oil recoveries will happen when the injector well is located in the zone where ascending permeability, capillary number greater than 4.81 × 10−6 and also fracture with the most deviation with pressure gradient line (i.e. angular pattern) are gathered in an area between the injection and production wells.