Flood-irrigated agricultural soils can be a significant source of the greenhouse gases (GHG) carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) (Linquist et al. 2011, Oertel et al. 2016). As these ecosystems are typically characterized by high spatial and temporal heterogeneity, continuous trace gas measurements are needed to better detect patterns and quantify net ecosystem fluxes. Measuring surface fluxes is challenging during periods of inundation, but exclusion of these periods is likely to significantly underestimate annual CH4 emissions, and potentially overestimate N2O effluxes. Here we report on modifications to a system of Eosense eosAC automated chambers, a Picarro G2508 greenhouse gas analyzer, and a modified insulated enclosure (Bonar Plastics) for continuous measurements in periodically inundated fields.