Vortex rock weirs (VRW) are often used in natural channel design applications to maintain channel form and function, provide physical channel stability, and enhance aquatic habitats. A balanced approach is required to address (often) conflicting goals of VRWs, which include providing erosion protection and grade control while facilitating fish passage for target species. This research evaluated a sequence of modified VRWs in a small-scale watercourse in Southern Ontario, Canada. To determine passage suitability for the target fish species, the water level, water temperature, and channel geometries at 10 VRWs and 11 adjacent pools were monitored under different water level conditions. The structural dimensions and velocity at each VRW were compared to the burst swim speed of local small-bodied fish species to determine fish passage suitability and identify the best practices for VRW design and construction. The results concluded that VRWs provided suitable passage for small-bodied fish species through gap and over-weir flow pathways, particularly during low water level conditions. Further, appropriate design considerations based on the VRW gradient, VRW width, keystone size, and pool length contributed to 100% fish ‘passability’ under all water level conditions. The methodology is provided for predicting the velocity and small-bodied fish passage suitability through VRWs, informing the best practices for VRW design and construction while balancing the requirements for channel stability and fish passage, and contributing to fish population management strategies.