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Abstract This study summarizes the results of structural, geochemical and seismological surveys carried out at Nisyros volcano (Aegean Sea, Greece) during 1999–2001. Field mapping and mesostructural measurements at the summit caldera (Lakki plain) indicate that faults follow two main strikes: NE-SW and N-S. The N-S striking fault depicts extensional features accommodating the left-lateral component of motion of the NE-SW- striking main faults. The NE-SW preferred strike of the Lakki faults and of the mineral-filled veins as well as the distribution and NE-SW elongation of the hydrothermal craters indicate that tectonics plays a major role in controlling the fluid pathway in the Nisyros caldera. The same NE-SW trend is depicted by CO2 anomalies revealed through detailed soil CO2 flux surveys, thus indicating a structural control on the pattern of the hydrothermal degassing. Degassing processes account for a thermal energy release of about 43 MW, most of which occurs at Lofos dome, an area that was affected by hydrothermal eruptions in historical times. The seismic study was conducted in June 2001, using a deployment specifically aimed at detecting signals of magmatic-hydrothermal origin. Our instruments recorded local and regional earthquakes, a few local long-period events (LP), and bursts of monochromatic tremor. Local earthquake activity is concentrated beneath the caldera, at depths generally shallower than 6 km. Plane-wave decomposition of tremor signal indicates a shallow (<200 m) source located in the eastern part of the caldera. Conversely, LP events depict a source located beneath the central part of the caldera, in the area of Lofos dome, at depths in the 1–2-km range. In agreement with geochemical and structural measurements, these data suggest that both the deeper and shallower part of the hydrothermal system are subjected to instability in the fluid flow regimes, probably consequent to transient pressurization of the reservoir. These instabilities may be related to input of hot fluids from the deeper magmatic system, as suggested by the variations in geochemical parameters observed after the 1997–1999 unrest episode. The significance of seismological and geochemical indicators as precursors of hydrothermal explosive activity at Nisyros is discussed.