Hot springs with associated Mn-Ag mineralization were identified in the intertidal zone of the Bahia Concepcion Bay of the central-eastern Baja California Peninsula. Hot spring activity is related to a system of NW-SE faults that are associated with the opening of the Gulf of California. The hot springs are hosted by Miocene volcanic and volcaniclastic units of the Comondu Group. The maximum discharge temperature recorded is 72 °C, with the pH ranging from 6.2 to 6.5 and salinity values reaching up to 27 g/kg. Veins, stockworks, breccias, crusts, and organosedimentary stromatolites of silica-carbonate and Mn oxides are associated with the hot springs. The Mn oxide and silica deposits show an association with Ag, As, Ba, Ca, Cu, Mg, Pb, Sb, Sr, Tl, V, W, and Zn. Acanthite and native silver occur along with pyrite in a mineral assemblage rich in opal-A, todorokite, romanechite, aragonite, high-Mg calcite, and barite. Three distinct mineral associations characterized by sulfides, sulfates, and oxides are recognized. The silver minerals formed late in the paragenesis. Textural evidence suggests a microbial mediation for the Mn mineral deposition. Pourbaix diagrams for Mn and Ag species were constructed for the physicochemical conditions of the coastal hot springs. These diagrams show that both Mn and Ag minerals are stable at low temperature (65 °C), and near neutral pH, under slightly reducing or oxidizing conditions. The characteristics of the subaerial to shallow submarine hot springs and the results of the geochemical modeling suggest that the hydrothermal system in the Bahia Conception Bay is formed through convection of meteoric waters, intermixed with some saline fluids or seawater.