Site factors predispose yellow-cedar (Chamaecyparis nootkatensis D. Don (Spach)) to a widespread climate-induced mortality in Southeast Alaska. We investigated the influence of canopy cover and snow on microclimate at two small watersheds across a range of declining yellow-cedar stands on Baranof and Chichagof Islands in Southeast Alaska. Two measures of canopy cover, derived from hemispherical photography and LiDAR, were correlated (r = 0.74 and 0.80) at the two sites; both had significant relationships (all R2 ≥ 0.61) with basal area of live trees on plots. Reduced canopy cover increases soil warming in spring and leads to rapid changes in air temperature. There is also a positive feedback where the loss of tree overstory due to yellow-cedar mortality contributes to open, exposed site conditions. Variable patterns of snow depth in late winter and spring at one of the sites, documented with daily remote photography, were associated with elevation and cover. Dead trees predominate where lethal shallow soil temperatures occurred but not where snow buffers these temperatures because of existing snow pack. Canopy cover estimates, landscape analysis, and snow modeling could provide the components for a regional risk model to identify areas in Southeast Alaska that are suitable and unsuitable for future conservation and management of yellow-cedar.