Nanostructured tungstates, such as CoWO4 and CuWO4, are very promising catalytic materials, particularly for photocatalytic oxidation of water. The high catalytic activity of tungstate nanoparticles partially is a result of their extremely small sizes, and, consequently, high surface‐to‐volume ratio. Therefore their properties depend strongly on the atomic structure, which differ significantly from that of the bulk material. X‐ray absorption spectroscopy is a powerful technique to address the challenging problem of the local structure determination in nanomaterials. In order to fully exploit the structural information contained in X‐ray absorption spectra, in this study we employ a novel evolutionary algorithm (EA) for the interpretation of the Co and Cu K‐edges as well as the W L3‐edge extended X‐ray absorption fine structure (EXAFS) of nanosized CoWO4 and CuWO4. The combined EA‐EXAFS approach and simultaneous analysis of the W L3 and Co(Cu) K‐edge EXAFS spectra allowed us for the first time to obtain a 3D structure model of the tungstate nanoparticles and to explore in details the effect of size, temperature and transition metal type.