It is necessary to estimate heavy metal concentrations within soils for understanding heavy metal contaminations and for keeping the sustainable developments of ecosystems. This study, with the floodplain along Le'an River and its two branches in Jiangxi Province of China as a case study, aimed to explore the feasibility of estimating concentrations of heavy metal lead (Pb), copper (Cu) and zinc (Zn) within soils using laboratory-based hyperspectral data. Thirty soil samples were collected, and their hyperspectral data, soil organic matters and Pb, Cu and Zn concentrations were measured in the laboratory. The potential relations among hyperspectral data, soil organic matter and Pb, Cu and Zn concentrations were explored and further used to estimate Pb, Cu and Zn concentrations from hyperspectral data with soil organic matter as a bridge. The results showed that the ratio of the first-order derivatives of spectral absorbance at wavelengths 624 and 564 nm could explain 52% of the variation of soil organic matter; the soil organic matter could explain 59%, 51% and 50% of the variation of Pb, Cu and Zn concentrations with estimated standard errors of 1.41, 48.27 and 45.15 mg • kg −1 ; and the absolute estimation errors were 8%-56%, 12%-118% and 2%-22%, and 50%, 67% and 100% of them were less than 25% for Pb, Cu and Zn concentration estimations. We concluded that the laboratory-based hyperspectral data hold potentials in estimating concentrations of heavy metal Pb, Cu and Zn in soils. More sampling points or other potential linear and non-linear regression methods should be used for improving the stabilities and accuracies of the estimation models.