Hydropower plays a very important role in European power systems. Consequently, any power system model aiming to reproduce the behaviour of current and future European power systems should include an accurate representation of the natural variability of water availability, i.e. the amount of water that can be transformed into energy. The JRC-EFAS-Hydropower dataset contains the weekly hydropower inflow of pure storage plants and the daily run-of-river generation for 27 European countries. The dataset is based on the river discharge provided by the European Flood Awareness System (EFAS) and on the JRC Hydropower Database. The discharge time-series for all the hydropower plants in a specific country are used as predictors for a ridge regression model calibrated on the actual data provided by the ENTSO-E Transparency Platform for the years 2015-2019. Then the model is used to extend the inflows and the generation to the entire time span available for the predictors, the years 1991-2019, reconstructing then the natural variability observed in the entire period.