Heavy metal and metalloid contamination of farmland soils are closely related to human health. Soil contamination caused by small-scale mining activities has been largely neglected, especially in developing countries. This research studies the characteristics and the source of heavy metals and metalloids in farmland soils in the Bailing Cu–Zn deposit area in Northeastern China through multiple approaches. Geochemical mapping conducted by portable X-ray fluorescence (pXRF) spectrometry and elemental fractionation analysis (sequential extraction) revealed the spatial variations in elemental concentration and fractionation of the farmland soils. The elemental variations in the sediment and water samples in a stream passing by the farmland were determined by inductively coupled plasma mass spectroscopy (ICP-MS) and inductively coupled plasma atomic emission spectroscopy (ICP-AES) analysis. Results indicate elevated As, Zn, Fe, and Mn concentrations in the west bank of the farmland and the associated environmental risks caused by extremely high As concentrations (>500 mg kg−1). The upstream mining activities are identified as a dominated source of contamination in the studied farmland based on the variations of elemental concentrations and fractionations, as well as multivariate analysis results. This study revealed potential ecological risks caused by heavy metal and metalloid contamination in farmland soils in the metal mine impacted area and the stream as a primary pathway for the migration of pollutants associated with mining activities.