Comprehending the temporal and spatial transitions of depositional processes in intertidal environments is of major importance to understanding sediment transport and the development of geomorphology in such environments. In this study, subsurface sediments were cored from the sandy tidal flat in the Kushida River estuary, Ise Bay, central Japan, and we investigated the three-dimensional distribution of sedimentary facies. In addition, we analyzed grain-size distribution using a settling tube method and determined the distribution characteristics for each sedimentary facies. As a result, three sedimentary units (Facies A–C) were recognized. Facies A, a wave-influenced deposit formed by the migration of sand bars, is characterized by a fine- to medium-grained sand layer showing weak coarsening upward or no grading with faint parallel lamination tendencies. Facies B; a channel-fill deposit influenced by fluvial forcing, consists of poorly sorted coarse- to medium-grained sand with a fining-upward trend. Facies C is a river flood deposit composed of mud or muddy sand, including a large amount of organic matter such as terrigenous plant debris. Grain-size analysis showed that Facies A and B are best discriminated by coefficient of variance (CV), a dimensionless value equal to a facies' sorting (standard deviation) divided by the mean grain-size of their respective grain-size distributions. Facies A has a low CV, indicating relatively well sorted sediments. Facies B has a higher CV, indicating relatively poor sorting. The CV value is thus expected to be an indicator of the degree of wave winnowing. Furthermore, the three-dimensional spatial distribution of sedimentary facies in subsurface sand was revealed using the CV values of facies' grain-size distributions as a proxy. We illustrate the temporal and spatial transitions of two main depositional processes, waves and fluvial currents, which control sediment transport and the development of geomorphology on the tidal flat. The CV may be an important proxy in facies analysis.