The β-emitting ⁹⁹Tc isotope is a high-yield fission product in ²³⁵U and ²³⁹Pu nuclear reactors, raising special concern in nuclear waste management due to its long half-life and the high mobility of pertechnetate (TcO₄⁻). Under the conditions of deep nuclear waste repositories, Tc is retained through biotic and abiotic reduction of TcO₄⁻ to compounds like amorphous TcO₂ ⋅ xH₂O precipitates. It is generally accepted that these precipitates have linear (Tc(μ-O)₂(H₂O)₂)_n chains, with trans H₂O. Although corresponding Tc−Tc and Tc−O distances have been obtained from extended X-ray absorption fine structure (EXAFS) spectroscopy, this structure is largely based on analogy with other compounds. Here, we combine density-functional theory with EXAFS measurements of fresh and aged samples to show that, instead, TcO₂ ⋅ xH₂O forms zigzag chains that undergo a slow aging process whereby they combine to form longer chains and, later, a tridimensional structure that might lead to a new TcO₂ polymorph.