Three long-offset transient electromagnetic (LOTEM) surveys werecarried out at the active volcano Merapi in Central Java (Indonesia) during the years 1998, 2000, and 2001. The measurements focused on the general resistivity structure of the volcanic edifice at depths of 0.5-2 km and the further investigation of a southside anomaly. The measurements were insufficient for a full 3D inversion scheme, which could enable the imaging of finely discretized resistivity distributions. Therefore, a stable, damped least-squares joint-inversion approach is used to optimize 3D models with a limited number of parameters. The mode ls feature the realistic simulation of topography, a layered background structure, and additional coarse 3D blocks representing conductivity anomalies. Twenty-eight LOTEM transients, comprising both horizontal and vertical components of the magnetic induction time derivative, were analyzed. In view of the few unknowns, we were able to achieve reasonable data fits. The inversion results indicate an upwelling conductor below the summit, suggesting hydrothermal activity in the central volcanic complex. A shallow conductor due to a magma-filled chamber, at depths down to 1 km below the summit, suggested by earlier seismic studies, is not indicated by the inversion results. In conjunction with an anomalous-density model, derived from arecent gravity study, our inversion results provide information about the southern geological structure resulting from a major sector collapse during the Middle Merapi period. The density model allows to assess a porosity range andthus an estimated vertical salinity profile to explain the high conductivities on a larger scale, extending beyond the foothills of Merapi.