Planning for the remediation of multiple threats is crucial to ensure the long term persistence of biodiversity. Limited conservation budgets require prioritizing which management actions to implement and where. Systematic conservation planning traditionally assumes that all the threats in priority sites are abated (fixed prioritization approach). However, abating only the threats affecting the species of conservation concerns may be more cost-effective. This requires prioritizing individual actions independently within the same site (independent prioritization approach), which has received limited attention so far. We developed an action prioritization algorithm that prioritizes multiple alternative actions within the same site. We used simulated annealing to find the combination of actions that remediate threats to species at the minimum cost. Our algorithm also accounts for the importance of selecting actions in sites connected through the river network (i.e., connectivity). We applied our algorithm to prioritize actions to address threats to freshwater fish species in the Mitchell River catchment, northern Australia. We compared how the efficiency of the independent and fixed prioritization approach varied as the importance of connectivity increased. Our independent prioritization approach delivered more efficient solutions than the fixed prioritization approach, particularly when the importance of achieving connectivity was high. By spatially prioritizing the specific actions necessary to remediate the threats affecting the target species, our approach can aid cost-effective habitat restoration and land-use planning. It is also particularly suited to solving resource allocation problems, where consideration of spatial design is important, such as prioritizing conservation efforts for highly mobile species, species facing climate change-driven range shifts, or minimizing the risk of threats spreading across different realms.