Groundwater resource is vital for industrial, drinking and irrigation purposes in the Dagujia river basin, China. The objective of this work was to comprehensively assess the hydrochemical characteristics and evolution processes of the Quaternary aquifer (QA) and the bedrock aquifer (BA) of the basin using statistical methods and hydrochemical plots. In total, 56 groundwater samples were collected from the QA (34 samples) and BA (22 samples). In addition, statistical methods combined with the geographic information system were used to identify the hydrochemical parameters of groundwater, as well as its spatial distribution in the Dagujia river basin. The Piper diagram showed that Ca-Na-HCO3 was the dominant groundwater facies type, while nine QA samples collected near the coastal line showed the Na-Cl facies type. On the other hand, the Gibbs diagram showed that most samples fell in the rock dominance zone. The principal component analysis results showed that the water–rock interaction and anthropogenic activities are the controlling factors, which is consistent with the results obtained using other methods. The results of this study indicated that rock weathering controls the hydrochemical characteristics of groundwater, while anthropogenic contamination and sea water intrusion are becoming increasingly serious issues for both QA and BA in the Dagujia river basin. Therefore, both Quaternary and bedrock aquifers require more attention.