These data are TDEP estimates of nitrogen deposition to Skaneateles and Owasco lakes and their watersheds, and for the continental US as a whole. They support the analysis in the manuscript "Atmospheric Ammonia Deposition: A Significant Source of Nitrogen to an Oligotrophic Lake and its Watershed" by D.P. Swaney,T.J. Butler, R.W. Howarth, R. Marino, G.M. Beachley, and C.B. Baublitz, submitted to JGR: Biogeosciences