While control over crystal structure is one of the primary objectives in crystal growth, the present lack of predictive understanding of the mechanisms driving structure selection precludes the predictive synthesis of polymorphic materials. We address the formation of off-stoichiometric intermediates as one such handle driving polymorph selection in the diverse class of MnO2-framework structures. Specifically, we build on the recent benchmark of the SCAN functional for the ab initio modeling of MnO2 to examine the effect of alkali-insertion, protonation, and hydration to derive the thermodynamic conditions favoring the formation of the most common MnO2 phases-β, γ, R, α, δ, and λ-from aqueous solution. We explain the phase selection trends through the geometric and chemical compatibility of the alkali cations and the available phases, the interaction of water with the system, and the critical role of protons. Our results offer both a quantitative synthesis roadmap for this important class of functional oxides, and a description of the various structural phase transformations that may occur in this system.