Soil water plays a crucial role in biogeochemical processes within karst ecosystems. However, geochemical variations of soil waters under different land covers and the related karst critical zone processes are still unclear. In this study, five land covers, including grassland, dry land, shrub land, reforestation land, and bamboo land in the Qingmuguan karst area of Chongqing Municipality, Southwest (SW) China were investigated in order to better understand the spatio-temporal variations of soil water geochemistry and its controlling mechanisms. The hydrochemistry of soil water and stable carbon isotopic compositions of dissolved inorganic carbon (δ13CDIC) in soil water were analyzed by a semi-monthly sampling strategy. The results show that there is remarkable spatio-temporal variation in the hydrochemistry and δ13CDIC of soil waters under different land covers in the studied area. Soil waters collected from shrub, dry, and afforestation lands have higher total dissolved solids (TDS), Ca2+, and HCO3− concentrations and heavier δ13CDIC, which is probably associated with the stronger carbonate dissolution caused by higher soil CO2 and carbonate content in soils under these land covers. However, lower TDS, Ca2+, and HCO3− concentrations as well as δ13CDIC values but higher SO42− concentrations are found in soil waters collected from bamboo land and grassland. The reason is that higher gypsum dissolution or oxidation of sulfide minerals and less soil CO2 input occurs in soils under these two land covers. Under the shrub, dry, and afforestation lands, higher concentrations of Ca2+ and HCO3− in soil waters occur in rainy seasons than in dry seasons, which are probably linked to higher CO2 input due to stronger microbial activities and root respiration in the wet summer seasons. In addition, seasonal variations of NO3− concentrations in soil waters from the dry land are observed, and much higher NO3− concentration occurs in the rainy seasons than that in the dry seasons, which suggest that the agricultural fertilization may lead to high NO3− in soil water. On the vertical soil profile, except for the bamboo land, soil waters under different land covers commonly show an increasing trend of main ion concentrations with the increase of depth. This vertical variation of hydrochemistry and δ13CDIC values in soil waters is primarily controlled by the intensity of carbonate dissolution related to carbonate content in soils and soil CO2 production. The soil waters under different land covers have great variations in δ13CDIC values which ranged from −20.68‰ to −6.90‰. Also, the [HCO3−]/([Ca2+] + [Mg2+]), [NO3−]/[HCO3−], and [SO42−]/([Ca2+] + [Mg2+]) molar ratios in soil waters show a large amplitude of variation. This suggested that carbonic acids could not be a unique dissolving agent and sulfuric/nitric acids may play a role in the weathering of carbonate in the Qingmuguan karst area.