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Around the world, peatland degradation and soil subsidence is occurring where these soils have been converted to agriculture. Since initial drainage in the mid-1800s, continuous farming of such soils in the California Sacramento-San Joaquin Delta (the Delta) has led to subsidence of up to 8 meters in places, primarily due to soil organic matter (SOM) oxidation and physical compaction. Rice (Oryza sativa) production has been proposed as an alternative cropping system to limit SOM oxidation. Preliminary research on these soils revealed high N uptake by rice in N fertilizer omission plots, which we hypothesized was the result of SOM oxidation releasing N. Testing this hypothesis, we developed a novel N budgeting approach to assess annual soil C and N loss based on plant N uptake and fallow season N mineralization. Through field experiments examining N dynamics during growing season and winter fallow periods, a complete annual N budget was developed. Soil C loss was calculated from SOM-N mineralization using the soil C:N ratio. Surface water and crop residue were negligible in the total N uptake budget (3 – 4 % combined). Shallow groundwater contributed 24 – 33 %, likely representing subsurface SOM-N mineralization. Assuming 6 and 25 kg N ha-1 from atmospheric deposition and biological N2 fixation, respectively, our results suggest 77 – 81 % of plant N uptake (129 – 149 kg N ha-1) was supplied by SOM mineralization. Considering a range of N uptake efficiency from 50 – 70 %, estimated net C loss ranged from 1149 – 2473 kg C ha-1. These findings suggest that rice systems, as currently managed, reduce the rate of C loss from organic delta soils relative to other agricultural practices.