The groundwater environment of wetland has been deteriorating under the strong interference of human activities in recent years. Because of the traditional evaluation methods for groundwater quality do not distinguish the effects of high natural background and anthropogenic pollution, the evaluation results can not represent the real state of water quality comprehensively, faithfully and reliably. Methods: In the study, the principal component analysis was developed for factor analysis. The scores of each sampling point were calculated based on the score and variance contribution of each factor. The comprehensive score under the influence of factors was calculated. Results: The comprehensive evaluation results showed that there were three main factors affecting groundwater in the study area. Factor 1 contained high Fe, Mn and Al caused by natural high background. Factor 2 contained NH+4, CODMn and NO-2 exceeding the standard caused by agricultural and domestic sewage. Factor 3 was I- pollution caused by a combination of natural and anthropogenic influences. Conclusions: The calculated comprehensive impact degree was consistent with the results of traditional water quality assessment. The score chart of comprehensive impact degree can not only evaluate groundwater quality, but also the natural and anthropogenic impacts on groundwater quality based on the identified factors.