Frequency analysis on extreme hydrological and meteorological events under the effect of climate change is performed in the island of Crete. Data from Regional Climate Model simulations (RCMs) that follow three Representative Concentration Pathways (RCP2.6, RCP4.5, RCP8.5) are used in the analysis. The analysis was performed for the 1985–2100 time period, divided into three equal-duration time slices (1985–2010, 2025–2050, and 2075–2100). Comparison between the results from the three time slices for the different RCMs under different RCP scenarios indicate that drought events are expected to increase in the future. The meteorological and hydrological drought indices, relative Standardized Precipitation Index (SPI) and Standardized Runoff index (SRI), are used to identify the number of drought events for each RCM. Results from extreme precipitation, extreme flow, meteorological and hydrological drought frequency analysis over Crete show that the impact of climate change on the magnitude of 100 years return period extreme events will also increase, along with the magnitude of extreme precipitation and flow events.