The study reveals the relationships between crystal-chemical and genetic properties of beryl from several rare-element granitic pegmatites of the LCT family from the Damara Belt, Namibia. Based on their chemical compositions, the studied beryl samples can be divided into two groups. Beryl from the first group (the Engelbrecht's and Etusis pegmatites) is poor in Fe, Mg and Mn; however, slightly enriched in Zn and alkali elements (Na > Li, Rb, Cs). The samples from the second group (Kuduberge and Tsaobismund) are slightly enriched in Fe and Mg, in which they are mostly charge-balanced by Na, while other octahedral and channel constituents are negligible. The affinity of the first group of beryl to the dominant tetrahedral substitution is manifested in cell dimensions and the c/a ratio. Based on Raman and infrared spectroscopy, the Kuduberge and Tsaobismund samples have a very similar position and intensity of water FTIR bands, indicating the presence of both water types in the channels. The Englebrecht's sample is similar, however, the Etusis sample exhibits a shift of H2O II ν1 band, which could be attributed to a smaller Na content and strong dominance of doubly coordinating water. Our results indicate preferential occupancy of Na in the octahedral Na + (Fe,Mg)2+ = + Al substitution, which is typical for beryl from less fractionated pegmatites (Kuduberge and Tsaobismund), however, Na can also be a part of the complex tetrahedral substitution found in Englebrecht's beryl. Higher concentrations of Mn, Sc and Ti indicate a less fractionated genetic environment due to their affinity to Mg and Fe2+, whereas Cs, Rb and Zn prefer tetrahedral substitution, which is typical in highly evolved pegmatites.