Various computer models have been developed to assist producers in planning manure and nutrient management programs. None of these models incorporates fixed costs associated with manure storage, hauling, and application. Current methods for calculating manure application rates require information such as nutrient content in manure, availability of nutrients for use as a fertilizer, and loss factors for different storage and application methods. The objective of this study was to develop a linear programming model that incorporates economic data on fixed and variable costs that can be linked to existing manure management computer models. An example with respect to swine (Sus scrofa) production is presented for various enterprise systems. As the size of the swine enterprise becomes greater than 150 sows, earthen lagoon storage and irrigation application becomes the optimal least cost method. Least cost storage and application costs for the 1200 sow operation was 63% of the least cost solution for the 150 sow operation. Within the same storage and application system, the 1200 sow operation had 77% of the per pig costs for a 300 sow operation. For enterprises with fewer sows, deep pit storage and injection application is the least cost choice.