São Paulo metropolitan region experienced an acute water crisis between 2013 and 2015. According to the Brazilian and international press, it was due to climatic, anthropogenic, and water management factors. This paper assesses the hydro-climatic characteristics of the crisis by focusing on the Alto-Tietê basin and the headwater of the Piracicaba-Capivari-Jundiaí (PCJ) basin that supply 70% of the water consumed in the metropolis. Based on 16 rain-gauge stations, 5 runoff-gauge stations, and several statistical analyses carried over the 1951–2015 period, this assessment shows that the 2013–2015 hydro-climatic crisis resulted from a large number of days without rain in the north of the Alto-Tietê basin and to less intense precipitation events in the headwaters of the PCJ basin during the austral spring 2013 and the year 2014. It also defines a return period of 98 years for observed river flows in 2014. Despite the rare nature of this hydrological drought, the need for efficient water saving policies is brought forward.