Watershed management is of utmost importance today, serving as a critical diagnostic unit for effectively overseeing, organizing, and planning our precious water resources. The primary aim of this study is to develop a hydrological management model for the Tarqui River basin in Cuenca, Ecuador. To achieve this, climate change scenarios were analyzed using the Hydro-BID tool, a resource for water resource planning and management in Latin America and the Caribbean. The study yielded significant findings, including basin morphometry parameters, data processing for precipitation, temperature, and flow obtained from stations near the basin, alongside their corresponding validations and consistency tests. The model was also simulated and calibrated using data from a hydrological station within the basin drainage area. Climate change scenarios were projected over 50 years, and the data were divided into percentiles to conduct simulations for each scenario. The outcomes facilitated the identification of the most favorable scenario and a comparison with the current simulation data. As a result, flow rates showed an increase of 5.23% and 9.51% over the current flow in optimistic scenarios (RCP 2.6 and RCP 4.5), while pessimistic scenarios (RCP 6.0 and RCP 8.5) indicated a decrease of up to −6.95% and −7.43%, respectively. Moreover, a notable variability in rainy seasons was detected, characterized by intense rainfall in shorter time frames than current flow patterns. It is essential to consider that the basin will change due to population growth, expansion of agricultural activities, and industrial and livestock development, potentially leading to water stress within the basin. Therefore, the relevant authorities must be ready to control and implement preventive and conservation plans for water sources, ensuring adequate water supply management for local communities.