The prominent problem in archetypal germanate glasses is the germanate anomaly where the density exhibits maxima at 15-20 mol % of the alkali oxide content. Here we report O-17 two-dimensional NMR spectra for GeO2 and Na-germanate glasses where the presence of both bridging oxygen linking Ge-[4] and highly coordinated Ge (Ge-[5,Ge-6]-O-Ge-[4]) and nonbridging oxygen, and an increase in topological disorder are demonstrated at the density maximum, manifesting atomic origins of the anomaly. These densification mechanisms in germanate glasses with Na content are remarkably similar to densification in v-B2O3 with pressure.