The use of distributed precipitation data in hydrological models is critically important to simulate processes at a micro-basin scale. However, aerial precipitation at a high resolution is required to run these models. This study aimed to set up the HydroBID tool in the Guadalquivir River basin using satellite-based precipitation products. The employed products included GSMaP gauge version 6, interpolated rain gauges using Kriging, the combined GS product for Bolivia, and the proposed combined product for the Guadalquivir basin. The GS Guadalquivir was generated by combining the satellite-based product GSMaP gauge version 6 with the local rain gauge network. The main difference with GS Bolivia is the improvement of the resolution from 5 km to 250 m. An iteration scheme using 230 micro-basins was employed, reaching a correlation of 0.98 compared to the control dataset. By using the hydrological model with the precipitation products, the daily river discharge was obtained, showing a high correlation of 0.99 and efficiency of 0.96 in relation to observed data between 2000 and 2016 at Obrajes station. Simulated flows with Kriging and GS Guadalquivir products presented similarly high correlations compared to the observed flows. In the case of GSMaP and GS Bolivia, these products showed general underestimations of the simulated flows, reaching correlations between 0.28 and 0.91, respectively. Moreover, annual volumes were analyzed, where the overestimation of GSMaP, Kriging, and GS Guadalquivir showed similar characteristics concerning the distribution of specific river discharges and volumes. Therefore, HydroBID appeared to be a feasible tool with enough adaptability to use distributed precipitation and simulate flows at a micro-basin scale. Therefore, we recommend applying this scheme to other basins to carry out analysis of events, water balance, and floods and similar studies.