Heavy metal pollution of farmland soils is a serious environmental problem. The accurate estimation of heavy metal pollution levels of farmland soils is very crucial for sustainable agriculture. Concentrations of heavy metal elements (As, Cd, Cr, Cu, Mn, Ni, Pb, and Zn) in farmland soils at 186 sampling sites in the Baghrash Lake Basin, NW China, were determined and analyzed based on the pollution index (Pi), the geo-accumulation index (Igeo), the enrichment factor (EF), the ecological risk index (ER), and the environmental risk index (Ier). The results of these five different estimation methods were compared and discussed. The obtained results indicated that the average concentrations of all the heavy metals in the farmland soils of the study area were lower than the Soil Environmental Quality of China (GB 15168-2018) levels, but the average concentrations of Cd, Cr, Ni, Pb, and Zn exceed the corresponding background values. Significant differences in estimation results existed between the five estimation methods. Based on the identified concentrations, the average Pi, Igeo, and EF values of the heavy metals in farmland soils decreased in the order of: Zn > Pb > Cd > Cr > Ni > Cu > As, whereas the average ER values decreased in the order of: Cd > As > Cu > Pb > Ni > Cr > Zn, and the average Ier values decreased in the order of: Cd > Cu > Zn > As = Pb > Cr > Ni. The pollution class values with different estimation methods were ranked as: Pi > Igeo = EF > ER = Ier. The obtained results suggest that the most appropriate estimation method and soil background values of farmlands should be used for better understanding the environmental quality of farmland soils. Overall, the EF and ER methods are recommended for assessing heavy metal pollution risks of farmland soils.