Many shale and limestone formations exhibit natural fractures in the form of calcite veins. Although these natural fractures might be sealed, they are prone to activation in hydraulic fracturing operation due to their low mechanical properties. Once these fracture are activated, the flow in such fractures without proppants play a role not only in production performance but also in analyzing the mechanisms responsible for the low recovery of water flowback. To address this issue, we created induced fractures within calcite veins of Niobrara formation using indirect tensile experiment and fracture permeability experiments were conducted by injecting both water and gas. The results of fracture permeability tests in Niobrara formation were compared with the results of fracture permeability tests in granite sample. The effective fracture permeability to water is significantly lower than the fracture permeability to gas in calcite veins while the fracture permeability of granite sample to both water and gas is almost similar. Comparing the fracture permeability of the Niobrara sample with the granite sample provides some insights into the possibility of water trapping microfractures as a possible reason for low water-flowback recovery. Besides the interaction of water with rock, fracture roughness can be another mechanism affecting fracture permeability. To this end, the topographic surface of samples were measured by laser profilometer and the fluid flow in rough fractures were simulated numerically to analyze the effect of roughness on fracture permeability.