Aerial line transect distance sampling surveys of coastal areas in the North Channel and Georgian Bay, Lake Huron, were conducted to estimate density of double-crested cormorants (Phalacrocorax auritus). Surveys were approximately every two weeks through summer from 2000 to 2005. In each year, density of cormorants declined towards late summer indicating a large scale outward migration of cormorants from Lake Huron. The seasonal pattern of decline differed between the two regions based on a mixed model analysis. Seasonal patterns in apparent fledging patterns may reflect differences between the North Channel and Georgian Bay in nesting phenology, nesting synchrony or some combination of these factors. Density was generally higher in the North Channel relative to Georgian Bay seasonally and during the period 2000–2002 likely reflecting higher per unit area productivity in the North Channel. In the years 2003–2005, density was lower in both regions and similar compared to earlier years of the survey likely reflecting a regime shift that occurred in Lake Huron at that time. The effect of this change was greater in the North Channel than in Georgian Bay as indicated by a greater decline in cormorant density in the North Channel after 2002.