The paper introduces a logical extension to data-based mechanistic (DBM) modeling, which provides hypothetico-inductive (HI-DBM) bridge between conceptual models, derived in a hypothetico-deductive manner, and the DBM model identified inductively from the same time-series data. The approach is illustrated by a quite detailed example of HI-DBM analysis applied to the well-known Leaf River data set and the associated HyMOD conceptual model. The HI-DBM model significantly improves the explanation of the Leaf River data and enhances the performance of the original DBM model. However, on the basis of various diagnostic tests, including recursive time-variable and state-dependent parameter estimation, it is suggested that the model should be capable of further improvement, particularly as regards the conceptual effective rainfall mechanism, which is based on the probability distributed model hypothesis. In order to verify the efficacy of the HI-DBM analysis in a situation where the actual model generating the data is completely known, the analysis is also applied to a stochastic simulation model based on a modified HyMOD model.