In order to gain insights on the conditions of aqueous alteration on asteroid Ryugu and the origin of water in the outer solar system, we developed the measurement of water content in magnetite at the micrometer scale by secondary ion mass spectrometry (NanoSIMS) and determined the H and Si content of coarse-grained euhedral magnetite grains (polyhedral magnetite) and coarse-grained fibrous (spherulitic) magnetite from the Ryugu polished section A0058-C1001. The hydrogen content in magnetite ranges between ~900 and ~3300 wt ppm equivalent water and is correlated with the Si content. Polyhedral magnetite has low and homogenous silicon and water content, whereas fibrous magnetite shows correlated Si and water excesses. These excesses can be explained by the presence of hydrous Si-rich amorphous nanoinclusions trapped during the precipitation of fibrous magnetite away from equilibrium and testify that fibrous magnetite formed from a hydrous gel with possibly more than 20 wt% water. An attempt to determine the water content in sub-μm framboids indicates that additional calibration and contamination issues must be addressed before a safe conclusion can be drawn, but hints at elevated water content as well. The high water content in fibrous magnetite, expected to be among the first minerals to crystallize at low water–rock ratio, points to the control of water content by local conditions of magnetite precipitation rather than large-scale alteration conditions. Systematic lithological variations associated with water-rich and water-poor magnetite suggest that the global context of alteration may be better understood if local water concentrations are compared with millimeter-scale distribution of the various morphologies of magnetite. Finally, the high water content in the magnetite precursor gel indicates that the initial O isotopic composition in alteration water must not have been very different from that of the earliest magnetite crystals.