The sources and primary mechanisms of high iodine concentration in deep groundwater are rarely reported, thereby restricting the development and utilization of the related groundwater resources. To address these issues, 194 deep groundwater samples were collected from the Zhangwei watershed in the North China Plain, China, to analyze their constituents including iodine. Statistics, principal component analysis and hydrological methods were employed to determine the distribution of iodine concentrations and their controlling hydrogeochemical processes. The results show that the iodine concentration ranged from 2 to 446 μg/L and generally increased along the groundwater flow direction. Three zones with high iodine concentration (> 20 μg/L) were delineated as the alluvial–proluvial plain (Zone A, average 70 μg/L), alluvial–lake plain (Zone B, average 83 μg/L) and coastal plain (Zone C, average 199 μg/L), respectively. In Zone A, aquifer minerals weathering probably releases iodate ions into groundwater. The iodate is reduced with nitrate as the electron acceptor of iodine and transported with the precipitation infiltrating through the vadose zone to recharge groundwater, resulting in increasing the groundwater iodine concentration. In Zone B, the iodine concentrations depend on the contents of the organic matter, clay minerals, and iron aluminum oxide in the alluvial–lake sediments, due to that the deeply buried organic matter is rich in iodine which is released into groundwater through the biodegradation of organic matter, In Zone C, the iodine is probably derived from the sediments which were deposited in Quaternary marine transgression events, and its enrichment was controlled by the strong reduction condition of the deep aquifers. In one word, the iodine sources and hydrogeological conditions determined the high iodine concentrations of deep groundwater in the studied watershed. These findings can provide foundation for further insight into the high iodine concentration of deep groundwater in other hydrogeological units of the North China Plain and other similar units over the world, thereby ensuring drinking groundwater safety.