Livestock manure is an important source of nutrients for crop production. However, farmers typically do not know the exact nutrient values for livestock manure. In many instances, manure has been viewed as a waste, and as a result it is applied close to the source resulting in over application of nutrients. Thus, the goal of nutrient application has often been applied to reduce the application expense rather than to maximize crop income. This results in wasted money and potentially negative impacts on water quality. Several livestock manure management scenarios were created based on agronomic nutrient requirements using the Utilization of Animal Manure as a Plant Nutrient (AMANURE) software to investigate water quality impacts with the National Agricultural Pesticide Risk Analysis (NAPRA) WWW modeling system. Application of manure at agronomic rates can result in high nitrate-nitrogen losses for some soil types, especially when applied in late fall. The application of manure at an agronomic rate does not necessarily equate to adequate water quality protection, and farmers must take care applying manure at agronomic rates, because nitrate-nitrogen loss potential varies spatially and temporarily. Nutrient loss probability maps for Indiana at 5%, 10%, 25%, and 50% values were created to demonstrate potential water quality impacts when livestock manure is applied to cropland at agronomic rates. The NAPRA WWW system coupled with AMANURE can be used to identify site-specific livestock manure management plans that are environmentally sound and agronomically appropriate.