We report a detailed structural disorder study of the Ba_xMn[Fe(CN)₆]2(x_+1)/3·zH₂O (x = 0 and 0.3) molecular magnets by carrying out Reverse Monte Carlo (RMC) simulations of neutron diffraction data. Both samples have also been investigated using X-ray diffraction, infrared spectroscopy and dc magnetization techniques. Rietveld refinement of X-ray and neutron diffraction patterns confirmed the single phase formation for both compounds in a face-centered cubic structure. IR spectral study establishes the presence of cyanide flipping in both compounds, thereby revealing inherent structural disorder in the compounds. A ferrimagnetic coupling of Mn²⁺ (S = 5/2) spins and the Fe³⁺ (S = 1/2) spins is found for both compounds. Results of RMC simulations of neutron diffraction data for both compounds show that: (i) around the coordinated oxygen atoms (located at the 24e crystallographic sites with [Fe(CN)₆] vacancies), there are formations of small clusters of non-coordinated oxygen atoms; and (ii) Ba substitution leads to a reduction in this structural disorder. The role of reduced water content as well as vacancies of [Fe(CN)₆] towards the observed reduction in the structural disorder is discussed.