Deficiencies of the micronutrients iodine and selenium are particularly prevalent where populations consume local agricultural produce grown on soils with low iodine and selenium availability. This study focussed on such an area, Gilgit-Baltistan in Pakistan, through a geochemical survey of iodine and selenium fractionation and speciation in irrigation water and arable soil. Iodine and selenium concentrations in water ranged from 0.01–1.79 µg L−1 to 0.016–2.09 µg L−1, respectively, which are smaller than levels reported in similar mountainous areas in other parts of the world. Iodate and selenate were the dominant inorganic species in all water samples. Average concentrations of iodine and selenium in soil were 685 µg kg−1 and 209 µg kg−1, respectively, much lower than global averages of 2600 and 400 µg kg−1, respectively. The ‘reactive’ fractions (‘soluble’ and ‘adsorbed’) of iodine and selenium accounted for < 7% and < 5% of their total concentrations in soil. More than 90% of reactive iodine was organic; iodide was the main inorganic species. By contrast, 66.9 and 39.7% of ‘soluble’ and ‘adsorbed’ selenium, respectively, were present as organic species; inorganic selenium was mainly selenite. Very low distribution coefficients (kd = adsorbed/soluble; L kg−1) for iodine (1.07) and selenium (1.27) suggested minimal buffering of available iodine and selenium against leaching losses and plant uptake. These geochemical characteristics suggest low availability of iodine and selenium in Gilgit-Baltistan, which may be reflected in locally grown crops. However, further investigation is required to ascertain the status of iodine and selenium in the Gilgit-Baltistan food supply and population.