The high concentration of iron and manganese in groundwater is harmful to human health, and the sources of manganese in rapidly urbanization areas are complex. Based on more than 2500 sets of hydrochemical data in different historical periods, the spatial distribution characteristics, sources, and genesis of groundwater manganese in different aquifers and areas with different urbanization levels in the Pearl River Delta were studied by using mathematical statistics and principal component analysis. The results showed that the concentration of manganese in groundwater in the pore aquifer was obviously higher than that in the fissure and karst aquifer. The proportion of high-manganese groundwater in the pore aquifer was twice that in the fissure and karst aquifer. The proportion of high-manganese groundwater in urbanized and suburban areas was significantly higher than that in non-urbanized areas. On a regional scale, the decomposition of organic matter and the reductive dissolution of Fe-Mn (oxygen) hydroxide in sedimentary strata under reductive conditions may have been the main factors controlling the increase in manganese concentration in pore aquifers. High-manganese groundwater in fissured aquifers may have been affected by low-oxygen domestic sewage leakage accompanying urbanization and industrial wastewater leakage and infiltration accompanying industrialization. The pore high-manganese groundwater was controlled by reduction conditions, and the weakly acidic environment of fissure and karst high-manganese groundwater was the important influencing factor. In the past 10 years, the groundwater environment in the study area has been improving, and the increase in groundwater redox potential and pH was not conducive to the formation of high-manganese groundwater, which was also the main cause of the overall decrease in Mn2+ concentration in groundwater of different types of aquifers in the process of urbanization.