Hydrological processes creating storage of groundwater beneath the earth surface is complex and functionally nonlinear. Hence more often required to be assessed using advanced numerical solution techniques. Accuracy in physics is attributed to the assumptions considered in correlating the point logs, whereas, mathematical precision depends upon, how close the discretized function approaches linearity. One of the major uncertainties in numerical modelling of the multi-aquifer domain, is the appreciation of the leakage that occurs into the interfaces between two layers. In the present paper, to address the problem, we take the opportunity of cluster wise lithological correlations and fitting of the exact Theim, Thies and Hantush solutions of pump test, to assess the vertical flows across the interfaces. We suggest that this technology be practiced for each layer of a multi-aquifer domain explicitly, and estimated vertical flows be used as an input to model application, in order to gain more certainty in the model results.