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• The 2016 earthquake in Central Italy reactivated normal faults with important coseismic ruptures. • The Nera River discharge increased followed by a fast depletion in 2017 and 2018 recession periods. • The increase in aquifer permeability seems affecting the post-earthquake river discharge. The 2016–2017 seismic sequence in Central Italy caused the reactivation of a complex NNW-SSE trending, WSW-dipping normal fault system associated with relevant coseismic ruptures. The seismic sequence significantly affected the groundwater circulation hosted in limestone aquifers. Based on the data available in May 2019, this work aims to contribute to understanding how the reactivation of the seismogenic faults has influenced the hydrological system of the upper Nera River basin. It appears that the seismic sequence changed the recession processes of the Nera River. Post-seismic recession curves are described by straight lines (non-darcian flow), while the pre-seismic ones follow the exponential function (darcian flow). After the earthquake, the system empties (i.e., the storage decreases) at a faster rate than before; this effect persists after more than two years from the 2016 earthquake. According to some geological cross-sections, the analysis of coseismic deformations and recession curves, a presumable increase in aquifer permeability seems to be the main factor affecting the post-earthquake river discharge. If the non-darcian recession process continues in the future, the river flow will be more variable than in the past, causing significant problems to water-using productive activities. This because, during prolonged drought periods, the fast decrease of the dynamic water storage would produce discharges lower than in the past. The results here reported can contribute to the understanding of the medium-long term evolution of this particular hydrological system as well as of other similar ones and could be useful to better managing the groundwater resources. [ABSTRACT FROM AUTHOR]