Metal–organic framework materials, as innovative functional materials for nonlinear optical technologies, feature linear and nonlinear optical responses, such as a laser damage threshold, outstanding mechanical properties, thermal stability, and optical transparency. Their non-centrosymmetric crystal structure induces a higher-order nonlinear optical response, which guarantees technological applications. ZnII– and AgI–squarate complexes are attractive templates for these purposes due to their good crystal growth, optical transparency, high thermal stability, etc. However, the space group type of the catena-((μ2-squarato)-tetra-aqua-zinc(II)) complex ([Zn(C4O4)(H2O)4]) is debatable, (1) showing centro- and non-centrosymmetric monoclinic C2/c and Cc phases. The same is valid for the catena-((μ3-squarato)-(μ2-aqua)-silver(I)) complex (Ag2C4O4), (2) exhibiting, so far, only a C2/c phase. This study is the first to report new crystallographic data on (1) and (2) re-determined at different temperatures (293(2) and 300(2)K) and the non-centrosymmetric Cc phase of (2), having different numbers of molecules per unit cell compared with the C2/c phase. There are high-resolution crystallographic measurements of single crystals, experimental electronic absorption, and vibrational spectroscopic data, together with ultra-high-resolution mass spectrometric ones. The experimental results are supported for theoretical optical and nonlinear optical properties obtained via high-accuracy static computational methods and molecular dynamics, using density functional theory as well as chemometrics.