This dataset contains four tables of estimates of the yearly sum of nitrogen and phosphorus inputs from fertilizer applications and from manure applications in selected watersheds in Chesapeake Bay drainage basin from 1950 to 2012. For the fertilizer data, county-level loads were used from three published sources. Data from 1950 to 1985 are from Alexander and Smith (1990). Data for the year 1986 are from Battaglin and Goolsby (1995). Data from 1987 through 2012 are from Brakebill, Gronberg, and Spahr (2016). These data were used in conjunction with 30-meter resolution land cover data from the National Land Cover Dataset for the year 2001 to distribute county-level fertilizer loads to cropland and summed by NHDPlus Version 1 catchments. Manure nutrient mass data for the Census of Agriculture years from 1950 to 2012 are from Gronberg and Arnold (2017). Formulae for calculating nitrogen and phosphorus mass per animal unit were also used from the Brakebill and Gronberg report. These data were used in conjunction with 30-meter resolution land cover data from the National Land Cover Dataset for the year 2001 to distribute county-level manure loads to pasture land and summed by NHDPlus Version 1 catchments. Eight digit hydrologic unit code identifiers are also included.