The Northern Refuge was established in 1985 as part of the lake trout Salvelinus namaycush rehabilitation effort for Lake Michigan. To evaluate progress toward lake trout rehabilitation in the Northern Refuge, we conducted annual (1991–2008) gill-net surveys in the fall to assess the adult population and beam trawl surveys in the spring to assess naturally reproduced age-0 lake trout. Our criteria for evaluating progress included the density of “wild” age-0 fish within the Northern Refuge, the proportion of wild fish within the adult population, density of spawners, adult survival, growth, and wounding rate by sea lampreys Petromyzon marinus. No wild age-0 lake trout were caught in the Northern Refuge during 1991–2008. Overall, wild lake trout did not recruit to the adult population to any detectable degree. The mean density of spawning lake trout decreased from 45 fish·305 m of gill net⁻¹·d⁻¹ during 1991–1999 to only 4 fish·305 m⁻¹·d⁻¹ during 2000–2008. Although the sea lamprey wounding rate more than doubled between these two time periods, catch curve analysis revealed that mortality of adult lake trout actually decreased between the two periods. Therefore, the 90% decrease in abundance of spawning lake trout between the two periods could not be attributed to increased sea lamprey predation but instead was probably due in part to the reduced lake trout stocking rate during 1995–2005. The paucity of natural reproduction in the Northern Refuge during 1991–2008 most likely resulted from alewife Alosa pseudoharengus interference with lake trout reproduction and from the relatively low lake trout spawner density during 2000–2008. Our results suggest that the annual stocking rate of lake trout yearlings should be increased to at least 250,000 fish/reef to achieve greater densities of spawners.