Abstract: Decision analysis was carried out to assess barrier and fishway options used to control Sea Lamprey (Petromyzon marinus) in the Laurentian Great Lakes. Tensions between use of in-stream barriers to control sea lamprey, and dam removal and provisioning of fishways to reduce habitat fragmentation of native fishes, are arising over a broad geographic scale of ecological and economic significance. Management objectives, barrier and fishway options, and key uncertainties influencing the expected performance of the options were specified in workshops with resource managers. Data syntheses and mathematical models were conducted to project proportional changes in population growth rates of sea lamprey and migratory non-target fishes for each option. Over a variety of circumstances, a permanent barrier with a trap-and-sort fishway best balanced sea lamprey control and non-target effects, but other options ranked higher in specific circumstances. Performance of the management options was sensitive to how fishery managers weight sea lamprey control versus nontarget effects. Adaptive management could be used to reduce uncertainty in the performance of different barrier and fishway options.