Mineral borates, the primary industrial source of boron, are found in a large variety of compositions. One such source, kernite (Na2B4O6(OH)2·3H2O), offers an array of challenges for traditional electron-probe microanalysis (EPMA)—it is hygroscopic, an electrical insulator, composed entirely of light elements, and sensitive to both low pressures and the electron beam. However, the approximate stoichiometric composition of kernite can be analyzed with careful preparation, proper selection of reference materials, and attention to the details of quantification procedures, including correction for the time dependency of the sodium X-ray signal. Moreover, a reasonable estimation of the mineral's water content can also be made by comparing the measured oxygen to the calculated stoichiometric oxygen content. X-ray diffraction, variable-pressure electron imaging, and visual inspection elucidate the structural consequences of high vacuum treatment of kernite, while Auger electron spectroscopy and X-ray photoelectron spectroscopy confirm electron beam-driven migration of sodium and oxygen out of the near-surface region (sampling depth ≈ 2 nm). These surface effects are insufficiently large to significantly affect the EPMA results (sampling depth ≈ 400 nm at 5 keV).