Coastal groundwater is an important resource in the developed region associated with human health and sustainable economic development. To identify the origins of salinity and evaluate the impact of water-rock interactions, seawater intrusion (SWI), and evaporation on groundwater in the coastal areas of Zhejiang and Fujian provinces, a comprehensive investigation was performed. Meanwhile, nitrate and fluoride indicators resulting from the anthropogenic activity and SWI were also considered. At last, the water quality index (WQI) of coastal groundwater was evaluated with geochemical and multivariate statistical methods. The results indicated that (1) the groundwater in coastal areas of Zhejiang and Fujian provinces has been affected by SWI to varying degrees. The analysis of selected ion ratios (Na+/Cl− and Br−/Cl−) and isotopic compositions showed that SWI is the predominant cause of increasing salinity in the groundwater of Zhejiang Province, while the cause is water-rock interactions (ion exchange and mineral weathering) in Fujian Province. The hydrochemical evolution path of groundwater in Zhejiang Province is Ca/Mg-HCO3 to Na-Cl, while a different pattern of Ca/Mg-HCO3 to Na (Mg/Ca)-Cl occurs in Fujian Province. However, the trend of SWI development in both provinces was freshening. (2) Nitrification, sewage infiltration, and SWI increased the NO3− content in groundwater. Some of the NO3− concentration in Fujian Province exceeds the standard, and the nitrogen pollution was more serious than in Zhejiang Province. The F− content in coastal groundwater was affected by SWI and mineral dissolution; the F− content in Zhejiang Province was higher than in Fujian Province, which was close to the groundwater standard limit. The average WQI value of Zhejiang was 103.61, and the WQI of Fujian was 61.69, indicating that the coastal groundwater quality in Fujian Province was better than in Zhejiang Province. The results of the study revealed the impact of SWI and anthropogenic activity on groundwater in the southern coastal zone of China and will be valuable for sustainable groundwater resource management.