One hundred and twenty-eight stream sediment samples were collected in the Misiones province of Argentina by the low-density geochemical mapping project of the China Geological Survey. The analyzed data were used to study the concentration, spatial distribution, local pollution level and potential ecological risk of eight heavy metals (As, Cd, Cr, Cu, Hg, Ni, Pb and Zn) by factor analysis, geoaccumulation index (Igeo), enrichment factor (EF) and the Hakanson’s potential ecological risk index (Eir and RI) methods. Results showed that the background values (median) of those elements were 2.97 ppm, 0.13 ppm, 212.60 ppm, 322.53 ppm, 0.013 ppm, 64.42 ppm, 12.58 ppm, and 198.85 ppm, respectively. Except for Hg, the contents of other elements were higher than the abundance of continental crust. The spatial distribution of Cu and Zn in stream sediments were consistent, while that of other elements were different. The factor analysis results implied that Cd, Cr, Cu, Ni and Zn were mainly affected by geological background and inherited the characteristics of regional parent rocks. Furthermore, Pb was not only controlled by natural conditions but also related to human activities, while As and Hg represented the anthropogenic sources, and their concentrations were affected by human activities. The results of Igeo and EF told us that Cu was heavily polluted in stream sediments; Pb and Zn were largely mildly polluted; As, Cr, Cd, Ni and Hg were mostly nonpolluted. The ecological risks were ordered as As > Cu > Cd > Pb > Hg > Cr > Ni > Zn. In general, the potential ecological risk of heavy metals in the Misiones province was low, but As and Cu also have a high ecological risk at some sampling points, which should be considered.