Nutrient management on livestock operations must be environmentally friendly, labor efficient, and cost effective. Poor nutrient management practices may lead to potential citizen complaints resulting in mitigation costs, fines or lawsuits. An econometric analysis of citizen complaints regarding surface water, groundwater, and odor concerns was completed to analyze farm characteristics affecting the probability of a verified citizen complaint. Farm compliance with environmental regulations involves policy uncertainty and sunk cost investments. A spreadsheet-based manure transport and land application decision tool, MANURE$HAUL, was developed to provide farmers, custom applicators, and others involved with the manure management a manure hauling capacity, time and cost calculator for liquid manure hauling systems using tractor-drawn tank spreaders and truck-drawn nurse tanks used in parallel with tractor-drawn tank spreaders. An optimal control theory model was used to model the uncertainty regarding the size of an animal air emission tax and its effects on a farmer's investment in emission-reducing technology.