Understanding the aqueous speciation of molecular metal-oxo clusters plays a key role in different fields such as catalysis, electrochemistry, nuclear waste recycling, and biochemistry. To accurately describe the speciation, it is essential to elucidate the underlying self-assembly processes. Herein, we apply a computational method to predict the speciation and formation mechanisms of polyoxovanadates, -niobates and -tantalates. While polyoxovanadates have been widely studied, polyoxoniobates and -tantalates lack the same level of understanding. In the first place, we proposed a pentavanadate cluster ([V5O14]3-) as a key intermediate for the formation of the decavanadate. Our computed phase speciation diagram is in particularly good agreement with the experiments. Secondly, we report the formation constants of the heptaniobate, [Nb7O22]9-, decaniobate, [Nb10O28]6-, and tetracosaniobate [H9Nb24O72]9-. Additionally, we have computed the speciation and phase diagram of niobium, which so far was restricted to Lindqvist derivates. Finally, we have predicted the formation constant of the decatantalate ([Ta10O26]6-) in water, even though it had only been synthetized in toluene. Furthermore, the corresponding speciation and phase diagrams for polyoxotantalates have been also calculated. Overall, we show that our method can be successfully applied to different families of molecular metal oxides without any need for readjustments; therefore, it can be regarded as a trustworthy tool for exploring polyoxometalates’ chemistry.