Prioritizing projects to improve cost‐effectiveness has become a common practice in natural resources management, especially in selecting sites for river restoration work. Previous studies for prioritizing road–stream crossing upgrade projects focused on either restoring river connectivity or reducing sedimentation, even though crossings can affect connectivity and sedimentation simultaneously. In this study, we simulated site selection to maximize the improvement of connectivity restoration and sedimentation reduction of three prioritization schemes targeting (a) river connectivity, (b) erosion risk, or (c) both objectives concurrently and compared the results. Furthermore, we examined the relationships between the cost‐effectiveness of prioritizations and watershed characteristics. We found significant differences among the effectiveness of prioritization objectives; thus, trade‐offs should be taken into consideration when prioritizing crossings. The incorporation of spatial interdependency among crossings and weighting objectives could significantly change the cost‐effectiveness. We also found that splitting the budget and using a portion to individually prioritize each objective could be more cost‐effective than using the whole budget to achieve concurrent objectives. Watershed characteristics like size and connectivity‐ and sedimentation‐related factors could be used to help identify effective management for both connectivity restoration and sedimentation control.