Abstract: Denitrification process of nitrate in aquifers is vital because it can dissipate groundwater nitrate pollution. It is very difficult to acquire the accurate denitrification rate in the aquifer due to the complicated hydrogeological conditions and hydrogeochemical environment in the field. A method was proposed for determining the denitrification rate in the aquifer based on in-situ pumping/injecting test and isotope technique. The method was applied in the groundwater innovation field base of Chinese Research Academy of Environmental Sciences, in the middle of the Chaobai River alluvial-proluvial fan. The method integrated the effect of actual hydrogeological conditions and hydrogeochemical environment on the denitrification process, as well as the effect of dilution and dispersion of nitrate in the aquifer. The results showed that the shallow aquifer, which was composed by sandy loam, was in the reducing environments at the depth of 26-28 m in the study area. The average nitrate concentration was 2.77 mg/L. The denitrification rates ranged between 349.52 and 562.99 μg/(kg·d) with the average value of 450.31 μg/(kg·d). The values were preliminarily verified to be reasonable by comparative study of domestic and foreign cases in the study area. The method of ignoring the intermediate products of NO₂^- and NO, perturbation sampling method, operation specification degree of N₂O and sampling frequency can result in the uncertainty of the denitrification rates. The method can objectively and quantitatively determine the denitrification intensity in the aquifer as a new idea. The research results can provide key data for studying the mechanism of nitrate fate and transport in the aquifer, and remediation and risk control of groundwater nitrate pollution.