We have developed a new method for the three-dimensional modeling of extended X-ray absorption fine structure (EXAFS) spectra which enables the extraction of the local structure of aqueous metal complexes from spectral mixtures of several components. The new method combines two techniques: Monte Carlo simulation and target transformation factor analysis (TFA). Monte Carlo simulation is used to create random arrangements between the X-ray absorbing metal ion and the ligand atoms, and to calculate the theoretical EXAFS spectrum of each arrangement. The theoretical EXAFS spectrum is then introduced as test spectrum in the TFA procedure, to test whether or not the test spectrum is likely to be a component of the spectral mixtures. This coupled procedure is repeated until the error in the test spectrum is minimized. The new method can thus be used to isolate and refine the structure of complexes from spectral mixtures and to determine their relative concentrations, solely on the basis of an estimate of a ligand structure. The performance of the proposed method is validated using uranium Liii-edge EXAFS spectra of binary mixtures of two uranium(VI) 3,4-dihydroxybenzoic acid complexes.