Water temperature is one of the main variables influencing freshwater organisms. In recent years, increasing water temperature trends have been observed in freshwater ecosystems worldwide. To assess the importance of such increases, they need to be put into context by studying long-term water temperature variability. However, it is often difficult to obtain a sufficiently long data series. This problem may be overcome by using data collected by different entities in different periods of time. However, this can lead to data comparability problems. In this paper, we present the process of reconstructing the annual mean water temperature series for the Ebro River at Escatron using data measured by the Escatrón power station, the Ebro Hydrographic Confederation and the Flumen research group. The data sources used different measurement methodologies and frequencies. Therefore, particular attention was paid to analysing the bias of the annual mean water temperature estimations calculated from the available historical data. A resampling methodology applied to 10-minute water temperature data was performed to assess the quality of the different estimators used to calculate the annual mean water temperature. Only one of the three estimators used could be considered to be unbiased. Another estimator could be corrected by estimating its bias. As a result, it was possible to reconstruct a water temperature series from 1949 to 2000, with a gap in the period 1978-1995. The series shows that there was an increase of 2.3◦C in the period 1955-2000.