This five-year study (2007–2011) investigated the impacts of canopy thinning, deer fencing, acorn production, and deer density on tree seedling recruitment in contrasting Quercus-Carya forests to explore the fate of mast and non-mast seedlings in different understory environments. It was conducted at the Mashomack Preserve on Shelter Island near the eastern end of Long Island, NY where tree regeneration in mature forests is very sparse due to extremely high deer (Odocoilus virginianus) populations. Forest thinning increased seedling density (mainly Q. alba L., C. glabra (Mill.) Sweet, Acer rubrum L. and Ostrya virginiana (Mill.) K. Koch) in both fenced and unfenced plots for the duration of the study. Fenced plots had higher total seedling density and taller white Q. alba seedlings than the unfenced plots. Four Quercus plus one Carya species had at least one mast year between 2007 and 2010 and generally during different years with variable impacts on seedling establishment. Acorn/nut production for all species was lowest in the fall of 2011 following nearly two years of drought. Quercus alba seedling density increased dramatically following a 2007 mast year, but had no further increase after a 2010 mast year. Deer density estimates ranged from 82–129 per km2 in 2007 to 2010, but dropped to 29 per km2 in 2011 associated with very low mast production. There was 100% removal of 260 exposed Q. velutina Lam acorns placed in both deer fenced and unfenced areas throughout the preserve, suggesting an important role of small mammals or birds. The results of this study suggest that mast year, canopy thinning and deer fencing, either individually or in concert, played a positive but variable role by increasing Quercus and Carya seedling establishment and sustainability.