The shallow groundwater of the quaternary system in the Baoshan basin, Yunnan Province is seriously polluted, threatening human health and restricting local socio-economic development; therefore, it is necessary to investigate the hydrochemical characteristics and formation mechanisms of the shallow groundwater of the quaternary system in the Baoshan basin. This study used EVS 2022 to establish a 3D visual geological model of the quaternary system in the basin and divided the shallow groundwater aquifers of the quaternary system into three groundwater systems, sampling 22, 9, and 4 groups in each groundwater system, respectively. Mathematical statistics, Piper’s trilinear diagram, Gibbs plots, the Gaillardet model, the ion ratio method, groundwater saturation, and the PCA-APCS-MLR model were used to analyze the groundwater hydrochemical characteristics and genesis of the study area. The results show the following: (1) The types of groundwater chemicals are mainly HCO₃-Ca-Mg type and HCO₃-Ca, the causes of the water chemical characteristics are mainly influenced by water–rock interaction and alternate cation adsorption, and the rock types with which the groundwater exchanges substances are carbonate rocks and silicate rocks. (2) The Fe²⁺, Mn²⁺, and NH₃-N contents in groundwater systems I and II exceed the standard, which is the human activity area, and groundwater pollution is mainly affected by human activities. (3) Four main categories of factors were obtained according to the PCA-APCS-MLR model, namely dissolution filtration, migration and enrichment factors, geological and human activity factors, and environmental factors and pollution factors; the cumulative contribution of variance was 77.84%, and the groundwater chemical characteristics were jointly influenced by hydrogeological conditions and human activities. The results of this study provide a basis for groundwater protection and management in the Baoshan basin, where groundwater system I is the key area for pollution and should be strengthened for control.

It is important to clarify the suitable ratio of well–canal combined irrigation and the suitable range for ecological groundwater depth for the ecological stability of the arid zone. The MODFLOW model was used to reconstruct long-term groundwater depth by analyzing the response relationship between vegetation cover and groundwater depth in the Weigan River irrigation district. The suitable range for ecological groundwater depth was obtained, and based on this range, the suitable well–canal combined irrigation ratio in the research area was further simulated. The results show the following: (1) The average annual depth of groundwater in 82.9% of the study area increased from 2012 to 2021, and the average annual depth of groundwater increased by 1.03 m in 2021 compared to 2012. The average depth of the groundwater in the upstream area increased the most, with an increase of 1.96 m. (2) The vegetation cover in the study area from 2012 to 2021 increased in general, with an increase of 0.0461 over the 10-year period, but it fluctuated between years. (3) The depth of the groundwater in the study area suitable for the growth of vegetation in the irrigation area ranged from 3 to 5 m, and the value of NDVI within this range concentrated near 0.564–0.731, which represents a good state of vegetation growth. (4) The ratio of combined well and canal irrigation in the study area from 2012 to 2014 surged from 0.13 in 2012 to 0.48 in 2014, and the irrational harvesting and replenishment relationship led to a rapid increase in the depth of buried groundwater. A suitable well–canal combined irrigation ratio of 0.396 in the study area was obtained. This study is beneficial for maintaining the sustainable development and utilization of water resources and ecological stability in the Weigan River irrigation district.