This paper aims to assess the influence of in situ stresses and geometry of the fracture surface on the behaviour of fluid flow through rock fractures. In this regard, fluid flow tests were performed on four mated, natural limestone fractures, under changing confining pressure ranging between 1.0 and 14 MPa. Based on the experimental observations, three types of relationship between pressure gradient and flow rate can be determined (linear, nonlinear induced by inertial effect and nonlinear induced by fracture dilation). Regression analyses of experimental data show that the nonlinearity induced by the inertial effect can be well quantified by the Forchheimer equation. The results of the experiments demonstrated that the confining pressure can change flow patterns from linear to nonlinear at higher flow rates, although by increasing the confining pressures the viscous and inertial coefficients in the Forchheimer equation show an increase of 10–40 and 2–10 times the initial magnitude, respectively. However, the rate of increase of the nonlinear coefficient b used in the Forchheimer equation steadily diminishes with the increase of confining pressure. The critical Reynolds number was successfully determined by taking a non-Darcy effect factor of 0.1, and the calculated critical Reynolds numbers show a decrease with further increase of the confining pressure and fracture roughness.