The Jialu River, a secondary tributary of the Huaihe River, has been severely contaminated from major contaminant sources, such as a number of untreated or lightly treated sewage waste in some cities. Groundwater along the river is not an isolated component of the hydrologic system, but is instead connected with the surface water. This study aims to investigate temporal and spatial variations in water chemistry affected by humans and to characterize the relationships between surface water (e.g. reservoirs, lakes and rivers) and groundwater near the river in the shallow Quaternary aquifer. Concentration of Cl⁻ in north Zhengzhou City increased prominently due to the discharge of a large amount of domestic water. Nitrate and potassium show maximum concentrations in groundwater in Fugou County. These high levels can be attributed to the use of a large quantity of fertilizer over this region. Most surface water appeared to be continuously recharged from the surrounding groundwater (regional wells) based on comparison surface water with groundwater levels, stable-isotopes and major ion signatures. However, the groundwater of a transitional well (location SY3) seemed to be recharged by river water via bank infiltration in September 2010. Fractional contributions of river water to the groundwater were calculated based on isotopic and chemical data using a mass-balance approach. Results show that the groundwater was approximately composed of 60–70% river water. These findings should be useful for a better understanding of hydrogeological processes at the river-aquifer interface and ultimately benefit water management in the future.