Naturally occurring reactive oxygen species (ROS) are widely involved in many environmental processes. Here we investigated the ROS generation associated with the interaction between complexed natural clay minerals (CMs) and dissolved organic matter (DOM). Our results showed that among the nine chemical-reduced CMs (CR-CMs), the light brown CR-CM (CR-CM 7) generated the highest ROS via oxygenation, relying on the reactive structural Fe(II) (Fe species that can transfer electrons to oxygen) instead of total structural Fe(II) as previously reported. Moreover, DOM affected the oxygenation of CR-CMs differently. The tight interaction between DOM and CR-CM 7 formed DOM-complexed Fe, while the weak interaction between DOM and the dark gold CR-CM (CR-CM 1) and the black CR-CM (CR-CM 5) exhibited decreased efficiencies. Mechanism studies revealed that ROS were generated through three pathways but all followed a similar one-electron transfer process in the presence of DOM. We further developed a three-layer geobattery model system and demonstrated that long electron transfer driven by CR-CMs/DOM could extend ROS generation to several centimetres across the oxic-anoxic interface, even without redox switching. These findings offer new insights into CMs-involved ROS generation and associated organic matter transformation in natural environments.