Although the overall atomic structure of a nanoscale crystal is in principle accessible by modern transmission electron microscopy, the precise determination of its surface structure is an intricate problem. Here, we show that aberration-corrected transmission electron microscopy, combined with dedicated numerical evaluation procedures, allows the three-dimensional shape of a thin MgO crystal to be determined from only one single high-resolution image. The sensitivity of the reconstruction procedure is not only sufficient to reveal the surface morphology of the crystal with atomic resolution, but also to detect the presence of adsorbed impurity atoms. The single-image approach that we introduce offers important advantages for three-dimensional studies of radiation-sensitive crystals.