Intensification of farming operations and increased nutrient application rates have led to higher crop yields and greater food security. At the same time, widespread use of commercial nitrogen (N) and phosphorus (P) fertilizers and large-scale livestock production have led to unintended environmental consequences, including eutrophication of both coastal and inland waters, threats to drinking water, and increased production of N2O, a potent greenhouse gas. In the past, crop and livestock production were typically more integrated, allowing most livestock to be fed by local crops, and most livestock manure to be applied directly to nearby cropland. Under current intensive agriculture practices, however, there is frequently a spatial decoupling of crops and livestock, leading to hot spots of manure production and a lack of opportunities for cost-efficient and environmentally sensitive disposal. In recent years, there has also been increased interest in the use of both farm and regional-scale bioreactors to convert excess manure to energy, thus exploiting a renewable energy source and increasing the potential to recycle animal waste. In the present work, I develop a spatially distributed optimization approach to identify hotspots of manure production, and, using both economic and environmental criteria, evaluate the economic feasibility of (1) transporting manure for spreading on cropland to meet established nutrient requirements, and (2) constructing biogas reactors to process excess manure in areas where long-range transport is found to be infeasible. This work is focused on manure redistribution, and potential for biogas construction at the continental US scale. In order to identify the spatial disconnect between livestock and crop production, I developed a gridded data set where each cell was 6 km x 6 km and calculated the crop requirements and manure production in each cell. After finding the P requirements in each cell, I found that 530,000 tonnes of phosphorus in manure was located in areas where, if applied, it would be in excess of the local crop requirements. I then examined the feasibility of transporting manure from excess locations (cells) to other locations to use as fertilizer by formulating an optimization problem to maximize the financial benefits of transporting the manure. Savings from transporting manure was calculated as the financial benefit from buying less mineral fertilizer minus the cost of transporting the manure. The solution to this optimization problem shows that transporting manure was able to reduce the excess phosphorus applied to fields by at least 88% with savings of up to $3 billion USD. Finally, I examined the costs and benefits of using the remaining excess manure (after transportation for fertilizer) as fuel to operate biogas plants. For this, I formulated an optimization model to site biogas plants across the continental US such that net profits from the biogas plants were maximized. Biogas net profits were defined as the money made from selling electricity minus the annualized costs for constructing and operating the biogas plants and transporting the manure to the biogas plants. The solution to this problem shows that constructing and operating 387 biogas plants yielded a net profit of $100 million USD and would utilize all of the manure remaining after transportation for fertilizer. This 100% utilization rate of excess manure would have great environmental benefits in terms of removing potential sources of non-point source pollution from farms that would otherwise be available to runoff into waterways.