Nutrient management plans are used to reduce non-point source pollution from animal operations. These plans require manure analysis and use indices to determine nutrient availability. This study evaluated a modified method for determining nitrogen fractions in swine slurry stored under slatted floors, calculating plant available nitrogen, and characterizing nitrogen fractions by holding pit depth. Manure samples were collected from gestating sow and finishing pig holding pits at discrete depths. Ammonium, amino acid, and amino sugar concentrations were significantly different for gestation holding pits by depth, but finishing pig holding pit values were not significantly different by depth. Plant available nitrogen was approximately 74% for gestation and 67% for finishing barn manures. Nitrogen fraction analysis suggests land application of swine manure for crop growth should be managed based on type of nitrogen present in the manure, which can be highly correlated to animal growth stage.