In this work, we reveal the coordination of copper ions absorbed by a series of covalent organic frameworks. The frameworks were synthesized through the nucleophilic substitution of either cyanuric chloride or phosphonitrilic chloride trimer by 4,4'-bipyridine, and they were utilized as absorbers for the removal of copper ions from aqueous solutions. The exfoliated counterpart of the layered network was compared to the bulk materials in terms of the copper retention capacity and efficiency. The ion absorption capacity of copper ranged from 100 to 290 mg/g depending on the morphology and chemical structure of the framework. As evidenced by the SEM and XRD analysis, the copper absorption induced certain morphological changes in the networks. EPR spectroscopy revealed the key finding of this study: the trigonal bipyramidal configuration of the copper ions in their divalent state, coordinated with the nitrogen of the core units, 4,4'-bipyridine, and chlorine ions. The analysis of the thoroughgoing experiments bridges the gap between coordination molecular chemistry and the field of covalent organic frameworks. EPR explores how the unique trigonal bipyramidal coordination could be suppressed in the end by the environment and, more specifically, by the addition of glycerol to the aqueous dispersions of the covalent organic frameworks.