The fate of phosphorus in groundwater needs to be understood because phosphorus-rich groundwater is discharged into surface water bodies, which causes eutrophication, especially in urbanized areas. The present study investigated the spatial distributions and driving forces related to the groundwater phosphate levels in various aquifers in the Pearl River Delta (PRD), which has undergone three decades of urbanization, as well as the relationship between groundwater phosphate and arsenic was also discussed. The results showed that most of the high-phosphate (>1.53 mg/L) groundwater occurred in granular aquifers. The proportion of high-phosphate groundwater in granular aquifers was more than four times that in fissured aquifers, whereas high-phosphate groundwater was not observed in karst aquifers in the PRD. High-phosphate groundwater primarily occurred in urbanized areas in the PRD, and the proportion of high-phosphate groundwater had a significant positive correlation with the urbanization level. In granular aquifers, reductive environment and alkalization led to enrichment of the groundwater with phosphate. Anthropogenic sources such as wastewater from township-village enterprises (TVE) and animal wastes were the main sources of high-phosphate groundwater in urbanized areas, and the external input of phosphate enriched the groundwater arsenic levels in urbanized areas. By contrast, geogenic sources such as the release of phosphate from the reduction of Fe/Mn (hydr)oxides and the seawater intrusion accompanied by the release of phosphate from secondary minerals were mainly responsible for the occurrence of high-phosphate groundwater in peri-urban and non-urbanized areas, respectively. The high concentrations of both phosphate and arsenic in groundwater in fissured aquifers were mainly attributed to the infiltration of wastewater from TVEs. In contrast to the granular aquifers, the groundwater Eh and pH conditions were not conductive to the occurrence of high-phosphate groundwater in fissured aquifers. Display omitted •Mostly high-phosphate groundwater occurs in granular aquifers in the PRD.•High-phosphate groundwater is positive correlation with the urbanization level.•Low Eh values and alkalization enhance groundwater phosphate in granular aquifers.•TVE wastewater and animal wastes are the main sources for high-phosphate groundwater.•External input of phosphate enhance groundwater arsenic enrichment in urbanized areas. Township–village enterprises wastewater and animal wastes were the main sources of high-phosphate groundwater in study area. Low Eh and high pH enhanced groundwater phosphate in granular aquifers.