Fluxionality is an important concept in cluster science, with far reaching implications in the area of catalysis. The interplay between intrinsic structural fluxionality and reaction-driven fluxionality though is underexplored in the literature and is a topic of contemporary interest in physical chemistry. In this work, we present an easy-to-use computational protocol combining ab initio molecular dynamics simulations with static electronic structure computations to ascertain the role of intrinsic structural fluxionality in the course of fluxionality occurring due to a chemical reaction. The reactions of structurally well-defined M3O6- (M = Mo and W) with water─which were originally used in the literature to illustrate the significance of reaction-driven fluxionality in transition-metal oxide (TMO) clusters, were chosen for this study. Besides probing the nature of fluxionality, this work provides the timescale for the key proton-hop step in the fluxionality pathway and further attests to the significance of hydrogen bonding in both stabilizing the key intermediates as well as driving forward the reactions of M3O6- (M = Mo and W) with water. The approach presented in this work becomes valuable given that the use of molecular dynamics alone may not help us in accessing some metastable states whose formation involves an appreciable energy barrier. Similarly, merely obtaining a slice of the potential energy surface via static electronic structure calculations will not be helpful in probing the different types of fluxionality. Hence, there is the need for a combined approach to study fluxionality in structurally well-defined TMO clusters. Our protocol may also serve as a starting point in the analysis of much more complicated fluxional chemistry happening on surfaces wherein the recently developed "ensemble of metastable states" approach to catalysis is deemed to be particularly promising.