The threat of water scarcity in the western United States and the contemporary issue of trace gas emissions from agricultural practices have stimulated the search for agricultural management alternatives to address water conservation and soil carbon sequestration. A field study in 2004 and 2005 in a processing tomato cropping system examines the potential of subsurface drip irrigation (SDI), conservation tillage (CT), and cover cropping (CC) in reducing carbon dioxide (CO2) and nitrous oxide (N2O) emissions. We hypothesize that root and soil respiration and, subsequently CO2 emissions, will be lower in the SDI system compared to furrow irrigation (FI), due to slower aggregate turn over and efficient water and nutrient delivery, via fertigation. We further hypothesize that N2O emissions will be reduced due to increased nitrogen efficiency in the SDI system. In addition, a combination of CT and CC with SDI will further enhance C sequestration due to increased C accumulation and a reduced rate in organic matter decomposition. To evaluate CO2 and N2O emissions among all the treatments, gas samples were taken approximately every 10 days before and after furrow irrigation events. Preliminary results show that on an annual basis the SDI had 4% less C emissions than in the FI and water use efficiency was approximately 50% greater in the SDI than the FI. Total respiration was consistently highest in the plant row within the SDI systems, whereas within the FI systems, the tomato bed shoulder had the greatest total respiration. There were no differences among treatments in N2O emissions 60 days after fertilizer was applied.