The magmatic–hydrothermal system of Kawah Ijen volcano is one of the most exotic on Earth, featuring the largest acidic lake on the planet, a hyper-acidic river and a passively degassing silicic dome. While previous studies have mostly described this unique system from a geochemical perspective, to date there has been no comprehensive geophysical investigation of the system. In our study, we surveyed the lake using a thermocouple, a thermal camera, an echo sounder and CO2 sensors. Furthermore, we gained insights into the hydrogeological structures by combining self-potential surveys with ground and water temperatures. Our results show that the hydrothermal system is self-sealed within the upper edifice and releases pressurized gas only through the active crater. We also show that the extensive hydrological system is formed by not one but three aquifers: a south aquifer that seems to be completely isolated, a west aquifer that sustains the acidic upper springs, and an east aquifer that is the main source of fresh water for the lake. In contrast with previous research, we emphasize the heterogeneity of the acidic lake, illustrated by intense subaqueous degassing. These findings provide new insights into this unique, hazardous hydrothermal system, which may eventually improve the existing monitoring system.