Vortex rock weirs (VRW) are often used in natural channel design applications to maintain channel form and function, provide physical channel stability, and contribute to habitat enhancement. A balanced approach is required to achieve conflicting goals of VRWs, which include providing erosion protection while allowing fish passage under various water level conditions. This research evaluated a sequence of asymmetrical rock weirs with 3-dimensional flow. Field assessments completed between June and September 2018 monitored water level, water temperature, and surveyed channel features at 10 rock weirs and 11 adjacent pools under different water level conditions. The structural dimensions and local velocity at each rock weir were compared to the swimming characteristics of local fish species to determine fish ‘passability’ and suggest best practices for rock weir design and construction. Results concluded fish passage occurs through gap and over-weir flow pathways and was most effective under low water level conditions. Further, appropriate design considerations based on rock weir gradient, rock weir width, keystone size, and pool length contributed to 100% fish passage effectiveness under all water level conditions. To address conflicting goals and the impact on fish passage for small-bodied fish species, methodology is provided for predicting local velocity and fish passage effectiveness through rock weir systems, inform best practices for rock weir design and construction while balancing the requirements for channel stability and fish passage, and contribute to fish population management strategies.