The Sacramento-San Joaquin Delta (California, U.S) has undergone soil loss due to subsidence since the peat lands were drained for agricultural use in the mid 1800's. The N2O emissions from a corn field on Twitchell Island, representing a common crop in the area, were quantified and compared to CH4 and N2O emissions from an adjacent rice paddy from 2010 to 2012. A nitrogen (N) fertilizer rate trial was conducted in the rice paddy in 2012 to test the hypothesis that increasing N rates would increase CH4 and N2O emissions. Additionally, the contributions of rice plants to soil C pools and subsequent CH4 emmissions was determined using a 13C pulse-labeling experiment carried out at reproductive growth (RG) and grain filling (GF) stages within the N rate trial. In the corn field, integrated N2O emission was quantified as 6.90, 10.40 and 5.03 kg N/ha for 2010, 2011, and 2012, respectively. For rice, integrated N2O emissions were 9.0, 4.80, and 5.78 kg N/ha, with integrated CH4 of 227.2, 38.7, and 133.82 kg C/ha for 2010, 2011, and 2012. Conversion to rice did not increase the GWP from N2O emissions, but it did increase GWP from CH4 emissions. In the rice field, GHG emissions and GWP were reduced after the first year. In the fertilizer rate trial, N rates had no effect on total CH4 and N2O emissions and GWP, with soil N mineralization likely providing enough N in the system. The 13C labeling experiment showed no effect of N treatment on the contribution of rice plants to porewater CH4 (pCH4), emitted CH4, and DOC, however, the higher nitrogen application rates of 160 resulted in greater plant contribution of dissolved inorganic carbon (DIC) than the 80 N rate in event 1. Plant derived carbon contributed up to 27% and 74% of emitted and porewater CH4, respectively, up to 9.1% to DOC, and from 13 to 78% towards DIC. Variations in plant contribution to these multiple pools reflected shifts in growing stages and changes in soil water levels. In all treatments, while positive N2O fluxes were observed, soils proved to be a weak net sink with an average of -0.199 mg N2O-N m−2 day−1. Methane emissions were highly variable but consistently positive with average emissions of 73.5 mg CH4 -C m−2 day−1. Contradicting our expectations, emissions of N2O and CH4 were not affected by nitrogen fertilization rates in this high organic matter soil.