Little is known about the processes taking place in new-born hydrothermal systems. We investigate the eruptive activity of Lusi, a sediment-hosted hydrothermal system active since 2006 in East Java, Indonesia. We show that superimposed on the regular geysering activity, Lusi features periods of enhanced hydrothermal processes during which boiling mud breccia is violently discharged from the eruptive vents. This results in sudden flooding lasting from several minutes to several hours and featuring almost instantaneous temperature peaks (i.e. from 35 °C to more than 65 °C in less than 2 min). Such activity (here named hydrothermal waves) is marked by high-frequency seismic radiations and is distinguished by sharp peaks of CH4 and CO2 concentrations in the erupted fluids. This suggests fluids upwelling from at least tents of meters below the near-surface. The injection into the shallow plumbing system of CH4- and CO2-rich batches of fluids may promote instabilities in the mud-breccia column leading to the hydrothermal waves. Our findings provide key insights into the deep charging dynamics of a new-born hydrothermal system and highlight the effects imposed by subtle variations in fluid-chemistry changes at depth.