Research on magnetic properties and chemical element content of environmental deposits has been conducted for various purposes. This study focuses on characteristic magnetic susceptibility, magnetic mineral morphology, and the elemental composition of Cangar and Padusan hot springs in the Arjuno-Welirang geothermal system to differentiate upflow and outflow systems, respectively. The measurements were performed for better understand the relation between magnetic susceptibility, Fe-Silicate content, magnetic mineral morphology, surface temperature and compare these characteristics in two kinds of hot springs in the same mountain system. Magnetic susceptibility ranged (7.558 - 62.694 ) × 10-6 m3/kg with an average of 30.651 × 10-6 m3/kg for Cangar (upflow) and (11.821 - 28.101) × 10-6 m3/kg with an average of 18.148 × 10-6 m3/kg for Padusan (outflow). In situ magnetic minerals extracted of hot springs are averaged of magnetic susceptibility is 26.981 × 10-6 m3/kg for Cangar and 24.445 × 10-6 m3/kg for Padusan. The element content dominated by Al, Si, K, Ca, Ti and Fe, where Fe is more abundant in Cangar as an upflow. The higher magnetic susceptibility, the greater of Fe-silicate content in both of hot springs. The surface temperature ranged from 38 - 48°C, where the higher temperature, the magnetic susceptibility increased. In Cangar, extracted magnetic minerals tend show crystalline, especially hedralic shape with very fine surface, clean and free of impurities. Meanwhile, some magnetic minerals are also found in spherical shapes, especially in Padusan.