Floods are natural phenomena that develop due to natural and/or anthropic factors actions. Floods are the most expensive environmental hazard in property damage costs and loss of life. El Niño-Southern Oscillation (ENSO) is an atmospheric phenomenon in the eastern equatorial Pacific Ocean. Scientific evidence shows that ENSO is decisive in Ecuador’s climatic behavior. GESTINA (GESTión INtegral del Agua) software is introduced. GESTINA is an early warning system for flooding. This software was designed for flood forecasting in extraordinary rainfall episodes. Its primary purpose is warning flood beginning based on rainfall intensity data registered. GESTINA was coded, including a geostatistical module to estimate flood flows for different return periods. The code was linked to HECRAS software to get additional hydraulic information. GESTINA receives precipitation data from a weather station in a constant increment time (5 min). Precipitation data is used for GESTINA to get runoff flow, water depth, flow velocity, and other hydraulic information. Every new precipitation data entered automatically updates hydraulic basin information. The comparison allows for forecasting the time at which a flood will occur. The software was applied in the Loja basin (Ecuador). Loja basin digital hydrological model was made. It was calibrated with historical city flood data. The difference between measured and calculated data is from 2 to 7%, and a 5% difference in flows measured at the Ecuadorian National Institute of Meteorology and Hydrology gauging station. GESTINA is a universal tool that will help predict floods in real time, avoiding the possibility of human and economic losses. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.