The Cauca River rises in the Colombian Andes and is the main tributary of the Magdalena River, which drains to the Caribbean Sea. The La Balsa station monitors the Upper Cauca basin and is located just downstream of La Salvajina hydroelectric facility. At this station, the discharge time series for November–January during 1950–2019 shows a statistically significant downward break, and change of distribution after 1986 has been documented after La Salvajina started operation. We assessed the spatio-temporal variability of hydroclimatology in the upper Cauca River basin during the pre- and post-Salvajina dam periods to better understand this break. Post-Salvajina, low (high) discharge events are linked to negative (positive) precipitation and soil moisture anomalies that are greater in magnitude and extension than those recorded in the pre-Salvajina period in response to the more intense El Niño events (more intense and frequent central La Niña events) after 1986. Therefore, it is necessary to consider possible future rainfall scenarios and non-infrastructure measures (i.e., reforestation, territorial planning, integrated watershed management, etc.) to mitigate floods and droughts impacts. The contribution of this study is to provide evidence for the need for foresight in the design of any structural or non-structural flood measures.