Aquatic organism passage barriers have been identified as one of the key impediments to recovery of salmonids and other migratory aquatic organisms in the Pacific Northwest of the United States. As such, state and federal agencies invest millions of dollars annually to address passage barriers. Because many barriers function as ad hoc grade control structures, their removal and/or replacement can unwittingly set off a cascade of effects that can negatively impact the very habitat and passage that project proponents seek to improve. The resultant vertical instability can result in a suite of effects that range from floodplain disconnection and loss of backwater and side channel habitat, to increased levels of turbidity. Risk assessment, including an evaluation of both the stage of stream evolution and a longitudinal profile analysis, provides a framework for determining if grade control is warranted, and if so, what type of structure is most geomorphically appropriate. Potential structures include placement of large wood and roughness elements, and constructed riffles, step-pools, and cascades. The use of structure types that mimic natural reach scale geomorphic analogues should result in improved aquatic organism passage, increased structural resilience, and reduced maintenance.