Francis turbines are often used for generating hydroelectric power, but their performance characteristics significantly depend on the operating conditions. In particular, interblade vortices in the passages between runner blades can occur at low flowrates, which can degrade performance, and increase vibrations and instability during operation. In a previous study, we showed that the hydraulic performance and flow characteristics depend on the flow passage area of runner blades under low-flowrate conditions. Under such operating conditions, the runner blade thickness can affect the interblade vortex characteristics, and in turn, affect the performance of the turbine. In this study, we investigated the effect of runner blade thicknesses in the presence of interblade vortices under low flowrates; steady- and unsteady-state Reynolds-averaged Navier–Stokes equations were solved using a shear stress transport as a turbulence model. The interblade vortices were described well at the near leading and trailing edges near the hub. These vortex regions showed flow separation and stagnation flow, and the interblade vortex characteristics were dependent on the high-magnitude unsteady pressures at the low-frequency region. For the same guide vane opening, at lower flowrates, higher blockage ratios reduced interblade vortex formation and unsteady pressure.