A series of tetra-n-butylammonium (TBA) salts of Zr-monosubstituted phosphotungstates of the Wells-Dawson structure (Zr-D) were prepared by varying pH in the range of 1.5‒4.5 during the synthesis. The compounds were characterized by elemental analysis, TGA, potentiometric titration, FT-IR spectroscopy, ³¹P NMR, and high-resolution ESI-MS. A combination of CHN analysis, thermogravimetry, and potentiometric titration with TBAOH point to different composition of the cationic sphere of Zr-D, namely the ratio of H⁺/K⁺, which increased with decreasing pH of the TBA salt precipitation. Spectroscopic studies (FT-IR, ³¹P NMR, and ESI-MS) implicated that the polyanion state in the Zr-D samples depends on the acidity. While Zr-D obtained at pH 1.5‒2.0 is a monomer, TBA_5.5K_0.5[α₂-P₂W₁₇O₆₁Zr(H₂O)₃], the samples prepared at pH 3.5‒4.5 have a dimeric structure, TBA₁₁K₃[{P₂W₁₇O₆₁Zr(μ-OH)}₂]·xH₂O (x = 7‒8), in the solid state, with a tendency to monomerization in dilute acetonitrile solutions producing [P₂W₁₇O₆₁Zr(μ-OH)]^7-. DFT simulations of the IR and NMR spectra show that the spectral changes originate from variations in the protonation state, hydration degree, and monomer–dimer speciation of the Zr-substituted Wells–Dawson polyanions. Catalytic properties of Zr-D were assessed in the oxidation of thioethers using H₂O₂ as oxidant. Zr-D prepared at pH 1.5‒2.0 and containing terminal Zr(H₂O) showed higher activity and sulfoxide yields than Zr-D with terminal Zr-OH prepared at higher pH values. A comparison of Zr-substituted polyoxotungstates of the Wells-Dawson, Keggin and Lindqvist structures revealed a correlation between catalytic activity and the polyanion charge density, which in turns modulates the local electronic environment of the Zr center.