In the Mediterranean arid region such as Southeast (SE) Spain, a considerable part of the fluvial network runs permanently dry. Here, many dry watercourses are embedded in catchments where agriculture has brought changes in carbon (C) and nitrogen (N) availability due to native riparian vegetation removal and the establishment of intensive agriculture. Despite their increasing scientific recognition and vulnerability, our knowledge about dry riverbeds biogeochemistry and environmental drivers is still limited, moreover for developing proper management plans at the whole catchment scale. We examined CO2 and N2O emissions in five riverbeds in SE Spain of variable agricultural impact under dry and simulated rewetted conditions. Sediment denitrifying capacity upon rewetting was also assessed. We found that, regardless of agricultural impact, all riverbeds can emit CO2 under dry and wet conditions. Emissions of N2O were only observed in our study when a long-term rewetting driving saturated sediments was conducted. Besides, most biogeochemical capabilities were enhanced in summer, reflecting the sensitiveness of microbial activity to temperature. Biogeochemical processing variation across rivers appeared to be more controlled by availability of sediment organic C, rather than by agriculturally derived nitrate. We found that the studied dry riverbeds, agriculturally affected or not, may be active sources of CO2 and contribute to transitory N2O emissions during rewetting phenomena, potentially through denitrification. We propose that management plans aiming to support ecosystem biogeochemistry through organic C from native vegetation rather than agricultural exudates would help to reduce anthropogenic greenhouse gases emissions and excess of nutrients in the watershed and to control the nitrate inputs to coastal ecosystems.