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This paper presents the analysis of a regional groundwater model via Feflow in tropical regions using two techniques: pilot points (PP) and constant zones (CZ). These methodologies allow the proper identification of biased parameters and heterogeneities of hydraulic properties. For this purpose, we developed a numerical density-variable model that is limited to reinterpreted data from real measurements. For the CZ, the initial parameters are considered constant; in contrast, in the PP technique, the initial parameters are assigned according to interpolations using in-situ point measurements. The developed model was applied in an area under the influence of the Inter-tropical Convergence Zone, located in the middle valley of Magdalena (MMV). This area is important in the development of Colombia due to its contribution to Gross Domestic Product, and it has been subject to significant changes in land use, as a result of intense economic activities. The established model shows a link between the observed state variable (hydraulic head) and hydraulic conductivity (K) proving the importance of spatial heterogeneity in K. The model is calibrated in order to establish K, the porosity and the specific storage capacity, reducing the mean square error of the state variable dependable on the observation points. The results show that the PP system approach provides a better heterogeneity representation and shows that each parameter is sensitive, and does not depend on other parameters. This research compiles the first breakthrough toward a methodology to assertively restrict a highly parameterized inverse regional model in a tropical basin. [ABSTRACT FROM AUTHOR]