Deltas provide many worthy ecosystem services. Yet, delta basins are quite vulnerable, especially in the face of climate change, which can affect the outcome of both agriculture and biodiversity. Moreover, rice paddy cultivation is well known to contribute with strong emissions of greenhouse gases (GHGs), such as methane (CH4). Thus, knowing the atmospheric variability of CH4 in relation to the different stages of the rice culture cycle could help to improve GHGs' mitigation strategies in deltas. The Ebro River Delta, in the northwestern Mediterranean basin, forms part of the largest Spanish river basin and is mainly covered by rice fields. In this study, for the first time, ground level (40 cm a.g.l.) atmospheric CH4 concentrations have been monitored in this area, through twenty-seven car mobile transects, over the course of one year. Seasonal, diurnal and spatial variability of CH4 concentrations were studied to identify its relationship with rice cultivation, meteorological conditions and land-use distribution. With regard to seasonal variability, autumn transects showed the highest mean values for atmospheric CH4 (2.466 ppm) when dead rice straw is mixed with the sediment, and weed growth is prevented. Spring and summer measurements gave the highest mean CH4 values at dawn (1.897e3.544 ppm), whereas autumn and winter produced the mean values after sunset (2.148e2.930 ppm). Spatial differences were accounted for by proximity to urban areas, presence of shallow water storage structures, and distance to seawater.