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Drought temporal characterization is a fundamental instrument in water resource management and planning of basins with dry-summer Mediterranean climate and with a significant seasonal and interannual variability of precipitation regime. This is the case for the Lower Guadiana Basin, where the river is the border between Spain and Portugal (Algarve-Baixo Alentejo-Andalucía Euroregion). For this transboundary basin, a description and evaluation of hydrological drought events was made using the Standardized Precipitation Index (SPI) with monthly precipitation time series of Spanish and Portuguese climatic stations in the study area. The results showed the occurrence of global cycles of about 25–30 years with predominance of moderate and severe drought events. It was observed that the current requirements of ecological flows in strategic water bodies were not satisfied in some months of October to April of years characterized by severe drought events occurring in the period from 1946 to 2015. Therefore, the characterization of the ecological status of the temporary streams that were predominant in this basin should be a priority in the next hydrologic plans in order to identify the relationships between actual flow regimes and habitat attributes, thereby improving environmental flows assessments, which will enable integrated water resource management.