Beryl, an economically significant mineral containing high concentrations of the critical metal Be, has been the subject of considerable characterization regarding its crystal structure and chemical composition. Despite this, discerning between alkali- and H2O-bearing beryls solely based on the alkali and water contents within the structural channels of beryl has remained a challenge. Additionally, the mechanisms that cause granitic melts to become enriched in Be remain ambiguous. Through comprehensive chemical and structural analyses of representative alkali-water-bearing beryl samples from Igla of East Egypt and Baishawo of South China, this contribution improves the beryl classification model and provides new perspectives on Be enrichment mechanisms. This analysis has demonstrated that a linear correlation exists between the water content and alkali content of hydrous beryls, and identified two distinct types of H2O molecules — Type I and II. Major elements are uniformly distributed throughout beryl grains, whereas trace elements exhibit core–rim zonation. Crystal–chemical characteristics of alkali- and water-bearing beryls provide valuable insights into pegmatite evolution, with implications for understanding mineralizing processes and formation conditions. The distributions of alkali metals, Mg, Mn and Fe in alkali-rich and H2O-rich (ARHR) beryl suggest that the pegmatite in the beryl-bearing zones is the product of magmatic metls. Low Fe/Mg ratios of alkali-poor and H2O-rich (APHR) beryl are associated with hydrothermal alkali-metasomatism. Using the Baishawo Be–Li–Nb–Ta pegmatite deposit as a case study, we utilize crystal fractionation simulations to demonstrate the alkali- and water-bearing beryls crystallized after high degrees of magma evolution. The study contributes to the classification of beryl varieties based on chemistry and structure, and provides new insights into Be enrichment mechanism in granitic melts and hydrothermal fluids.