Spent nuclear fuel contains heavy element fission products that must be separated for effective reprocessing for a safe and sustainable nuclear fuel cycle. 93Zr and 99Tc are high‐yield fission products that co‐transport in liquid‐liquid extraction processes. Here we seek atomic‐level information of this co‐extraction process, as well as fundamental knowledge about ZrIV (and HfIV) aqueous speciation in the presence of topology‐directing ligands such as pertechnetate (TcO4−) and non‐radioactive surrogate perrhenate (ReO4−). In this context, we show that the flat tetrameric oxyhydroxyl‐cluster [MIV4(OH)8(H2O)16]8+ (and related polymers) is dissociated by perrhenate/pertechnetate to yield isostructural dimers, M2(OH)2(XO4−)6(H2O)6 ⋅ 3H2O (M=Zr/HfIV; X=Re/TcVII), elucidated by single‐crystal X‐ray diffraction. We used these model compounds to understand the pervasive 93Zr‐99Tc coextraction with further speciation studies in water, nitric acid, and tetrabutylphosphate (TBP) ‐kerosene; where the latter two media are relevant to nuclear fuel reprocessing. SAXS (small angle X‐ray scattering), compositional evaluation, and where experimentally feasible, ESI‐MS (electrospray ionization mass spectrometry) showed that perrhenate/pertechnetate influence Zr/HfIV‐speciation in water. In Zr‐XO4 solvent extraction studies to simulate fuel reprocessing, we provide evidence that TcO4− enhances extraction of ZrIV, and compositional analysis of the extracted metal‐complexes (Zr‐ReO4 study) is consistent with the crystallized ZrIV2(OH)2(ReVIIO4−)6(H2O)6⋅dimer.