The nucleation process of zeolitic imidazolate frameworks (ZIFs) is, to date, not yet completely understood, making the search for tailored materials very difficult. Recently, it has been shown that, during the formation process, the symmetry of the precursors is reduced by ligand elimination and substitution reactions. The octahedral precursors with simple ligands, such as water, methanol, and/or NO3–, are transformed to five- and finally four-coordinated complexes with imidazole ligands. This reduction of symmetry, caused both by the changing coordination environment and distortions from the perfect symmetry leading to another point group, will have a large influence on the electronic structure and more specifically on the d-orbital splitting. This, in turn, will affect the d–d electronic excitations, which can be followed using UV–vis spectroscopy and which can help to unravel the formation process. In this work, we systematically investigate how the lowering of the number of ligands affects the symmetry and thus the geometry and electronic structure of Co2+ complexes with six, five, and four aqua ligands. Therefore, we first resort to qualitative techniques, such as crystal field theory (CFT) and ligand field theory (LFT), which reveal that the orbital splitting is characteristic for the number of ligands. However, as these techniques are not capable of providing quantitative results without the use of experimental data as input, we perform various computational calculations. Both average of configuration (AOC) and unrestricted density functional theory (UDFT) are thoroughly investigated, and we will determine which technique is the best suited to properly describe the ground state of these systems. To investigate the dependency on the d-orbital occupation, we also investigated V2+, Mn2+, and Ni2+ hexa-aqua-complexes and compared them to the Co systems.