The Qujiang River Basin is a significant water system located in Zhejiang Province, China, that serves as a primary water source for Quzhou City. For this research, we collected and examined water samples from the Qujiang River Basin. In this study, we collected and analyzed water samples from the Qujiang River Basin and employed a combination of methods, including water balance analysis; Piper trilinear diagram; Gibbs diagram; and environmental tracer techniques, such as hydrochemical and isotopic analysis. These techniques helped us to analyze the spatial distribution patterns and evolutionary trends of surface water and groundwater hydrochemistry, along with the stable isotopes of hydrogen and oxygen, as well as to determine the sources of surface water and groundwater by calculating the conversion ratio between surface water and groundwater. (1) The findings of our study indicate that the primary hydrochemical types in the study area are Ca-HCO3 and Ca-HCO3·Cl, with the ion composition of water primarily influenced by rock weathering and precipitation. (2) Similar spatial variations in hydrochemical indicators were observed between surface water and groundwater in the study area, with frequent transitions between the two. (3) The hydrogen and oxygen isotope content increases downstream, signifying that both groundwater and surface water in the study area are replenished by atmospheric precipitation, as supported by the relationship between hydrogen and oxygen isotopes and the meteoric water line. (4) We determined that groundwater predominantly replenishes surface water in the upstream area. The average contribution rate of groundwater to surface water is 19.67%, with an annual average recharge volume of 1.23 × 106 m3. Midstream and downstream, surface water mainly recharges groundwater, with an average contribution rate of 22.77% and an annual average recharge volume of 1.59 × 106 m3.