The presence of impervious surfaces in catchments interferes with the natural process of infiltration, which has a marked influence on the hydrological cycle, affecting the base flow in rivers and increasing the surface runoff and the magnitude of flood flows. Like many Latin American cities, Loja (located in southern Ecuador) has experienced significant rates of urban growth in recent years, increasing the impervious surfaces in the catchment where it belongs. The aim of this study is to analyze the spatiotemporal dynamics of imperviousness in the study area for the period 1989–2020, using the Normalized Difference Impervious Surface Index (NDISI) and the supervised classification of Landsat images. The effect on flood flows was studied for each timestep using HEC-HMS hydrological model. Additionally, a future scenario of impervious surfaces was generated considering the observed spatiotemporal variability, possible explanatory variables, and logistic regression models. Between 1989 and 2020, there was an increase of 144.12% in impervious surfaces, which corresponds to the population growth of 282.56% that occurred in the same period. The period between 2001 and 2013 was the one that presented the most significant increase (1.06 km2/year). A direct relationship between the increase in impervious surfaces and the increase in flood flows was observed, reaching a significant variation towards the horizon year that could affect the population, for which measures to manage the surface runoff is necessary.