Peculiar iron and manganese deposits coating walls, floors and ceilings of many galleries are one of the special features of the El Soplao Cave (Cantabria, Spain). These speleothems appear to have been deposited over wall clay deposits, as well as forming part of flowstones. Structure of crusts is essentially amorphous but several manganese and iron oxides were identified like goethite and birnessite, though all occur with a low degree of crystallinity. In the outer layer of the crusts, alteration iron minerals appear that derive from previous minerals in a process probably mediated by microorganisms. EDX microanalyses report fairly high values of Fe and Mn in the crusts, though the Mn/Fe ratio varies considerably as a function of distance from the substrate/bedrock. The present study proposes a genetic model for crust speleothems in El Soplao, based on oscillations of the phreatic level. The origin of these deposits is related to mobilization, under phreatic conditions, of polymetallic sulfides in the host rock. Metal ions (including Fe²⁺ and Mn²⁺) released into the cave under reducing conditions, are oxidized and fixed in a process mediated by bacteria, giving rise to oxides and hydroxides of low crystallinity. The presence of various black intercalated layers in aragonite flowstones indicate periods when cave conditions suddenly changed from vadose, when aragonite is precipitated, to phreatic and epiphreatic conditions, when the Mn-Fe deposits are precipitated. Subsequently, vadose conditions were re-established, leading to the final stages of precipitation of aragonite recorded in the flowstone and recent aragonite helictites on the surface of the Mn-Fe crusts.