Elucidating the formation process of 3-D arrays from submicrometer-sized particles is a key to creating an optimal fabrication process of photonic crystals. In this research, the spontaneous sedimentation of silica spheres is imaged by in situ confocal laser scanning microscopy, and the dynamics is studied. When the pH is 7.0 and 10, the rate of the formation process of a hexagonal structure is attributed to the transport of spheres in the early stage of precipitation, and can be reproduced by a simple equation for Langmuir-type adsorption, ignoring the desorption part. In a later stage, however, the rate becomes smaller. In the first layer, even after drying, the nearest two spheres are separated, while maintaining a hexagonal structure. From the results, the formation process of three-dimensional arrays from silica spheres is illustrated.