A cosmic-ray soil moisture probe is usually calibrated locally using soil samples collected within its support volume. But such calibration may be difficult or impractical, for example when soil contains stones, in presence of bedrock outcrops, in urban environments, or when the probe is used as a rover. Here we use the neutron transport code MCNPx with observed soil chemistries and pore water distribution to derive a universal calibration function that can be used in such environments. Reasonable estimates of pore water content can be made from neutron intensity measurements and by using measurements of the other hydrogen pools (water vapor, soil lattice water, soil organic carbon, and biomass). Comparisons with independent soil moisture measurements at one cosmic-ray probe site and, separately, at 35 sites, show that the universal calibration function explains more than 79% of the total variability within each dataset, permitting accurate isolation of the soil moisture signal from the measured neutron intensity signal. In addition the framework allows for any of the other hydrogen pools to be separated from the neutron intensity measurements, which may be useful for estimating changes in biomass, biomass water, or exchangeable water in complex environments.