We study partitions (equitable, externally equitable, or other) of graphs that describe physico-chemical systems at the atomic or molecular level; provide examples that show how these partitions are intimately related with symmetries of the systems; and discuss how such a link can further lead to insightful relations with the systems’ physical and chemical properties. We define a particular kind of graph partition, which we call Chemical Equitable Partition (CEP), accounting for chemical composition as well as connectivity and associate it with a quantitative measure of information reduction that accompanies its derivation. These concepts are applied to model molecular and crystalline solid systems, illustrating their potential as a means to classify atoms according to their chemical or crystallographic role. We also cluster materials in meaningful manners that take their microstructure into account and even correlate them with the materials’ physical properties.