We present a novel approach to investigate variations in upper mantle and transition zone (MTZ) water content based on the joint analysis of electromagnetic (EM) signals originating in the ionosphere and magnetosphere. We inverted EM signals (period range 6 hours–85 days) to probe the electrical conductivity structure underneath 20 geomagnetic observatories, accounting for the complex spatial structure of the ionospheric and magnetospheric sources. The joint inversion of EM data for the daily and long-period bands led to a significantly improved model resolution in the upper mantle and MTZ. The conductivity profiles reveal significant lateral variability, which we interpreted in terms of upper mantle and MTZ water content by a stochastic coupling of electrical conductivity with constrains on the mantle thermo-chemical structure derived from the analysis of seismic data. Our results suggest the existence of a relatively dry MTZ beneath Europe and a water-enriched MTZ underneath North America and northern Asia.