Nitrate contamination of groundwater systems used for human water supplies is a major environmental problem in many parts of the world. Fertilizers containing a variety of reduced nitrogen compounds are commonly added to soils to increase agricultural yields. But the amount of nitrogen added during fertilization typically exceeds the amount of nitrogen taken up by crops. Oxidation of reduced nitrogen compounds present in residual fertilizers can produce substantial amounts of nitrate which can be transported to the underlying water table. Because nitrate concentrations exceeding 10 mg/L in drinking water can have a variety of deleterious effects for humans, agriculturally derived nitrate contamination of groundwater can be a serious public health issue. The Central Valley aquifer of California accounts for 13 percent of all the groundwater withdrawals in the United States. The Central Valley, which includes the San Joaquin Valley, is one of the most productive agricultural areas in the world and much of this groundwater is used for crop irrigation. However, rapid urbanization has led to increasing groundwater withdrawals for municipal public water supplies. That, in turn, has led to concern about how contaminants associated with agricultural practices will affect the chemical quality of groundwater in the San Joaquin Valley. Crop fertilization with various forms of nitrogen-containing compounds can greatly increase agricultural yields. However, leaching of nitrate from soils due to irrigation has led to substantial nitrate contamination of shallow groundwater. That shallow nitrate-contaminated groundwater has been moving deeper into the Central Valley aquifer since the 1960s. Denitrification can be an important process limiting the mobility of nitrate in groundwater systems. However, substantial denitrification requires adequate sources of electron donors in order to drive the process. In many cases, dissolved organic carbon (DOC) and particulate organic carbon (POC) are the primary electron donors driving active denitrification in groundwater. The purpose of this chapter is to use a numerical mass balance modeling approach to quantitatively compare sources of electron donors (DOC, POC) and electron acceptors (dissolved oxygen, nitrate, and ferric iron) in order to assess the potential for denitrification to attenuate nitrate migration in the Central Valley aquifer.