This study presents a methodology for the regional parameters estimation of the SWAT (Soil and Water Assessment Tool) model, with the objective of estimating daily flow series in the Pacific drainage under the context of limited hydrological data availability. This methodology has been designed to obtain the model parameters from a limited number of basins (14) to finally regionalize them to basins without hydrological data based on physical-climatic characteristics. In addition, the bootstrapping method was selected to estimate the uncertainty associated with the parameters set selection in the regionalization process. In general, the regionalized parameters reduce the initial underestimation which is reflected in a better quantification of daily flows, and improve the low flows performance. Furthermore, the results show that the SWAT model correctly represents the water balance and seasonality of the hydrological cycle main components. However, the model does not correctly quantify the high flows rates during wet periods. These findings provide supporting information for studies of water balance and water management on the Peruvian Pacific drainage. The approach and methods developed can be replicated in any other region of Peru.