Metal–organic framework materials show feature linear- and nonlinear optical responses such as laser damage threshold, outstanding mechanical properties, thermal stability, and optical transparency as innovative functional materials for nonlinear optical technologies. The non-centrosymmetric crystal structure is precondition for generation of second-order nonlinear optical response, which guarantees technological applications. The ZnII- and AgI-squarate complexes are attractive templates for these purposes due to good crystal growth, optical transparency, high thermal stability, etc. However, debatable is the space group type of catena-((μ2-squarato)-tetra-aqua-zinc(II)) complex ([Zn(C4O4)(H2O)4]) (1) showing centro- and non-centro-symmetric monoclinic C2/c and Cc phases. The same is valid to catena-((μ3-squarato)-(μ2-aqua)-silver(I)) complex (Ag2C4O4) (2) exhibiting, so far, only C2/c phase. This study reports first new crystallographic data on (1) and (2) re-determined at different temperatures (293(2) and 300(2)K) and non-centro-symmetric Cc phase of (2), having different number molecules per unit cell comparing with 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. Experimental results are supported for theoretical optical and nonlinear optical properties obtained via high accuracy quantum chemical static methods and molecular dynamics, using density functional theory as well as chemometrics.