Modifying broiler diets to mitigate water quality concerns linked to excess phosphorus (P) in regions of intensive broiler production has recently increased. Our goals were to evaluate the effects of dietary modification, using phytase and reduced non-phytate phosphorus (NPP) supplementation, on P speciation in broiler litters, changes in litter P forms during long-term storage, and subsequent impacts of diets on P in runoff from litter-amended soils. Four diets containing two levels of NPP with and without phytase were fed to broilers in a three-flock floor pen study. After removal of the third flock, litters were stored for 440 d at their initial moisture content (MC; 24%) and at a MC of 40%. Litter P fractions and orthophosphate and phytate P concentrations were determined before and after storage. After storage, litters were incorporated with a sandy and silt loam and simulated rainfall was applied. Phytase and reduced dietary NPP significantly reduced litter total P. Reducing dietary NPP decreased water-extractable inorganic phosphorus (IP) and the addition of dietary phytase reduced NaOH- and HCl-extractable organic P in litter, which correlated well with orthophosphate and phytic acid measured by 31P nuclear magnetic resonance (NMR), respectively. Although dry storage caused little change in P speciation, wet storage increased concentrations of water-soluble IP, which increased reactive P in runoff from litter-amended soils. Therefore, diet modification with phytase and reduced NPP could be effective in reducing P additions on a watershed scale. Moreover, efforts to minimize litter MC during storage may reduce the potential for dissolved P losses in runoff.