Forest harvesting can impact site quality by removing essential nutrients, exacerbating the effects of historic base cation losses associated with acid deposition. We studied the 30-year trajectory of forest recovery from clearcutting (whole-tree harvest (WTH)) in a forest originally dominated by sugar maple (Acer saccharum Marsh.). At both the watershed scale (21.9 ha) and the “detailed” plot scale (1 m2), a dramatic decline of sugar maple was observed, along with maintenance of American beech (Fagus grandifolia Ehrh.) and an increase in birch, mainly yellow birch (Betula alleghaniensis Britt.). Many of the “detailed” plots where sugar maple failed to recruit became unoccupied rather than being “won” by another species. The decline of sugar maple was most severe in the upper elevation zones of the watershed, where low base status (especially Ca) of the soils was a likely driver. The results support previous studies indicating that regeneration by sugar maple is severely compromised on base cation depleted soils. Lower survival of seedlings for sugar maple emphasized the importance of maintaining advance regeneration to favor desired species such as sugar maple. Foresters should consider that sites with low base saturation and exchangeable Ca are likely to exhibit regeneration failure for sugar maple in the long term, even those with initial dominance by this species.