In climate and atmospheric science changes are constantly observed in hydro-meteorological patterns. These changes are normally associated with seasonality and climate variability and change. In recent years it has been documented and observed that climatic variability influences hydrological processes; however, these influences have not yet been incorporated in models, which have been assumed as stationary and invariant to climatic conditions. In this study the temporal variability of hydrological processes and their influence on the water balance of a mountainous basin in Chile (Chillan River basin) are observed and further modeled. A conceptual water balance model integrated with the Monte Carlo Analysis Toolbox (MCAT) is used to perform the analyses. Analyses such as the General Identifiability Analysis (GIA) and Dynamic Identifiability Analysis (DYNIA) were used. As a result we concluded that DYNIA, through the temporal sensitivity of each model parameter, helps us to observe the temporal variability of hydrological processes in different time periods throughout the year and moreover helps to improve the mathematical formulation of a conceptual model. This analysis contributes to a better understanding of hydrological processes in Andean watersheds, and thus would reduce uncertainties in the outputs of hydrological models under scenarios of climate change and/or variability.