Geothermal manifestations can enrich surrounding water and soil with trace metals, raising safety concerns for medicinal plants harvested from such areas. This study provides the first integrated assessment of Pb, Cd, Cu, Cr, Fe, and Zn in water, soil, and Melastoma malabathricum (L.) at two active hydrothermal sites within the Gunung Kembar geothermal zone, Aceh Province, Indonesia. Concentrations were determined by flame atomic absorption spectrometry (FAAS) using a validated external-calibration method, and soil-to-plant transfer was evaluated through bioconcentration factors (BCF). Method validation confirmed analytical reliability for Pb (recovery 84.09%), Cu (98.15%), and Fe (110.61%), while Cd, Zn, and Cr were treated as semi-quantitative due to matrix interference. Concentrations followed a consistent water < plant < soil gradient, identifying soil as the principal long-term reservoir governing plant exposure. Pb in M. malabathricum reached 0.317–0.393 mg/kg, exceeding the BPOM Regulation No. 9/2023 medicinal-plant threshold of 0.300 mg/kg at both sampling sites, and the estimated daily intake under a traditional-use scenario reached approximately 13% of the EFSA/JECFA BMDL₀₁ for cardiovascular effects. BCF values for Pb, Cu, and Fe (0.0016–0.0085) placed the species within the excluder category rather than within accumulator or hyperaccumulator ranges. The combination of supra-threshold tissue Pb with excluder-range BCF is not replicated in other Acehnese geothermal medicinal plants and constitutes the novel, public-health-relevant contribution of this work. Pre-use contaminant screening is recommended before medicinal preparation.