AbstractGreenhouse Gas Emissions (GHG) from two cropping systems on Twitchell Island was monitored spring 2010 to spring 2012. The island is one of 57 manmade Islands located in the San Joaquin-Sacramento Delta in California (herein the "Delta"). The cropping systems under study were field corn and Delta rice. The project was set to study the effects of the cropping system on GHG emissions and soil organic carbon (SOC). Carbon Dioxide (CO2), Methane (CH4) and Nitrous Oxide (N2O) emissions measurement was done every one to three weeks during spring 2010-2012. Crop final biomass and total carbon (C) was measured for residue and C input estimation each year. In addition, the effect of crop residue levels on GHG emissions and C dynamics was studied over one year in each system during 2010-2011. The main objective of this study was to test the hypothesis that conversion of subsided agricultural peat land from the current corn system to Delta rice would reduce overall GHG emissions, mainly CO2 and N2O. It was hypothesized that the increase in CH4 emissions due to the flooding conditions would be insignificant relative to total reduction in CO2 emissions.The Delta rice CH4 cumulative emissions differed between the two years of study (212 and 39 kg CH4 C/ha for the 2010-2011 and 2011-2012 year, respectively). The reduction in 2011-2012 vs. 2010-2011 CH4 emissions was likely due to the placement of rice residue 20-30cm below soil surface when the field was moldboard plowed in spring 2011 and the shorter flooding period during the 2011 rice growing season (108 vs. 82 days in 2010 and 2011, respectively). In an experiment to determine the effects of various levels of rice residue on CO2 and CH4 emissions, CH4 emissions from plots receiving rice residues averaged as much as 3 times higher than plots with no residue, while CO2 emissions were not affected. During both years, a significant percentage of the CH4was emitted during the winter field drain in preparation for spring planting (63% and 53% in 2010-2011 and 2011-2012 respectively). Total CO2 emissions in the rice system averaged slightly lower during 2010-2011 than in 2011-2012 (8044kg CO2 C vs. 9860kg CO2 -C/ha), respectively with over 70% of the emissions occurring when the field was not flooded. These figures are likely an overestimation, as they do not take into account the diurnal temperature fluctuation where soil respiration is lower at night. Total N2O emissions were higher in the rice system during 2010-2011 than 2011-2012 (11 kg N2O-N/ha and 6 kg N2O-N/ha in 2010-2011 and 2011-2012 respectively). All GHG emissions were related to flooding regime and soil water status, and were highest after the winter drain and during the period of field operations to summer flood for rice growing.In the corn system, total CO2 emissions were similar in 2011-2012 and 2010-2011 (8845 and 8405 kg CO2-C/ha respectively) with about 60% of it occurring during the corn growing period. N2O emissions averaged higher in the 2nd year of the study (8.9 vs. 12.6 kg N2O-N/ha in the 2010-2011 and 2011-2012 periods, respectively). N2O emissions from the corn system were also affected by soil water status, and were highest in the spring during a period of drop in water table levels. Residue level did not affect CO2 or N2O emissions in the cornfield. Total estimated residue carbon input from both systems was similar in 2011 (circa 5 metric tons C/ha) but was higher in the corn system in 2010 (circa 5 and 9 metric tons C /ha in the rice and corn systems respectively). In 2011 the corn residue was baled and removed, which left an estimated 1 ton C/ha from residue input. Both systems are a net source of GHG. A significant portion of the rice GHG emissions occurred during the fallow period and when the rice was planted but not flooded (i.e. pre-flood and drain process). In the corn system, GHG emissions occurred during the summer (CO2) and spring (N2O). Rice total GHG emissions (in CO2 equivalents) were higher in 2010-2011 but not significantly different in 2011-2012 than the corn system. Although the rice did not significantly reduce CO2emissions, while increasing CH4, it offers a system with more room for management improvements for GHG and subsidence mitigation. N2O emissions consisted of 50% to 75% of the annual GWP in CO2 equivalents in the two years (excluding CO2 emissions) in the rice system. A management practice that reduces N2O emissions would greatly reduce the total GHG. Lengthening the period the field is flooded in the winter, and shortening the drainage periods can significantly reduce N2O and CO2 emissions. But the possible increase in CH4emissions should be considered. Also, summer mid-season drain is likely reduce CH4 emissions during the summer flooding period and possibly during the fall drainage. The shortening of the drainage period can be achieved by actively pumping water out of the drainage ditches instead of letting the water percolate down, although the energy cost and effect on drain water DOC content should be considered. Improving agronomic management practices, such as variety selection for higher yield and lower days to harvest would shorten the period for CH4 emissions during the summer. Lastly, better crop establishment would improve crop uniformity, which again would lead to shorter time to harvest and guaranty higher yields.