Results of investigations of natural waters (drip and fracture) and speleothem moonmilk from the karst Proschalnaya Cave (Russia, Far East) are reported. Concentrations of Fe and Mn in drip water were highest in spring, while the concentration of Mn was lowest in the fracture water, which may be due to the nature of infiltration of water through different channels after spring snowmelt and autumn rains. Molecular genetics investigation of the moonmilk mass revealed the presence of iron bacteria of the genera Rhodoferax and Geothrix. The visually plastic and homogeneous mass of moonmilk was shown to be highly heterogeneous, containing various microstructures. Tubular microstructures had a richer elemental composition (C, O, Ca, Fe, Mn, Si, Al, and S), in comparison with claviform formations (C, O, Ca, and Na). Binding matrix in the composition of moonmilk is represented by reticular structures similar to nanofibers. The results of this research conducted in a monsoon climate may be interesting for speleologists working with karst caves in other climatic conditions.