Anaerobic digestion of manure and other agricultural waste streams with subsequent energy production can result in more sustainable dairy operations; however, importation of digester feedstocks onto dairy farms alters previously established carbon, nutrient, and salinity mass balances. Salt and nutrient mass balance must be maintained to avoid groundwater contamination and salination. To better understand salt and nutrient contributions of imported methane-producing substrates, a mass balance for a full-scale dairy biomass energy project was developed for solids, carbon, nitrogen, sulfur, phosphorus, chloride, and potassium. Digester feedstocks, consisting of thickened manure flush-water slurry, screened manure solids, sudan grass silage, and feed-waste, were tracked separately in the mass balance. The error in mass balance closure for most elements was less than 5%. Manure contributed 69.2% of influent dry matter while contributing 77.7% of nitrogen, 90.9% of sulfur, and 73.4% of phosphorus. Sudan grass silage contributed high quantities of chloride and potassium, 33.3% and 43.4%, respectively, relative to the dry matter contribution of 22.3%. Five potential off-site co-digestates (egg waste, grape pomace, milk waste, pasta waste, whey wastewater) were evaluated for anaerobic digestion based on salt and nutrient content in addition to bio-methane potential. Egg waste and wine grape pomace appeared the most promising co-digestates due to their high methane potentials relative to bulk volume. Increasing power production from the current rate of 369 kW to the design value of 710 kW would require co-digestion with either 26800 L d(-1) egg waste or 60900 kg d(-1) grape pomace. However, importation of egg waste would more than double nitrogen loading, resulting in an increase of 172% above the baseline while co-digestion with grape pomace would increase potassium by 279%. Careful selection of imported co-digestates and management of digester effluent is required to manage salt and nutrient mass loadings and reduce groundwater impacts.