Primarily associated with soil fertility management practices, nitrous oxide (N2O) is a potent greenhouse gas (GHG) whose emission from farmland is a concern for environmental quality and agricultural productivity. In California, agriculture and forestry account for 8% of the total GHG emissions, of which 50% is accounted for by N2O (CEC, 2005). Furrow irrigation and high temperatures in the Central Valley, together with conventional fertilization, are ideal for the production of food, but also N2O production. These conditions can promote N2O emissions, but also suggest great potential to reduce N2O emissions by optimizing fertilizer and irrigation management. Smaller, more frequent fertilizer applications increase the synchrony between available soil nitrogen (N) and crop N uptake and may result in less N loss to the atmosphere. Given that the ecosystem processes regulating the production of N2O respond to and interact with multiple factors influenced by environmental and managerial conditions, it is not always feasible to approach the study of integrated agricultural systems and their affect on GHG emissions by use of a factorial experiment alone. On-farm studies are therefore an important precursor to research station trials to determine which management practices and components of a complete management system should be targeted and isolated for future study. Farm-based trials also provide a realistic evaluation of current management practices subject to practical and economic constraints. The following study took place on existing farms in order to assess the effect of active, operational farm field conditions and current managements on GHG emissions and to thoroughly characterize two typical management systems. In this study, I determined how management practices, such as fertilization, irrigation, tillage, and harvest, affect direct N2O emissions in tomato cropping systems under two contrasting irrigation managements and their associated fertilizer application method, i.e. furrow irrigation and knife injection (conventional system) versus drip irrigation, reduced tillage, and fertigation (integrated system). Field sites were located on two farms in close proximity, on the same soil type, and were planted with the same crop cultivar. This project demonstrated that shifts in fertilizer and irrigation water management directly affect GHG emissions. More fertilizer was applied in the conventional system (237 kg N ha−1 growing season−1) than the integrated system (205 kg N ha−1 growing season−1). The amount of irrigated water was comparable between the two systems; 64 to 70 cm was applied in the conventional system and 64 cm in the integrated system. Total weighted growing season emissions were 3.4 times greater in the conventional system (2.39 ± 0.17 kg N2O-N ha−1) than the integrated system (0.58 ± 0.06 kg N2O-N ha−1), with a higher tomato yield in the integrated system (131 vs. 86 Mg ha−1). The highest conventional N2O emissions resulted from fertilization plus irrigation events and the first fall precipitation. In the integrated system, the highest N2O fluxes occurred following harvest and the first fall precipitation. Environmental parameters of soil moisture, soil mineral N, and dissolved organic carbon (DOC) were higher and more spatially variable in the conventional system. Reduced N2O emissions in the integrated system, resulting from low soil moisture, mineral N concentrations, and DOC levels, imply that improved fertilizer and water management strategies can be effective in mitigating greenhouse gas emissions from agriculture.