Shallow waters in tropical island and atoll regions are highly dynamic environments where sediment grain size characteristics and distribution are influenced by complex interactions. This research aims to obtain a description of the grain size characteristics of shallow water sediments on Kapota Island and Kapota Atoll, Wakatobi. Shallow water sediment samples were collected using a core pipe at 14 observation stations representing both study locations. Sediment grain size analysis was performed using the dry sieving method, while the fraction composition, sediment texture, and statistical parameters were determined with the aid of Gradistat software. The analysis results show that the shallow water sediments at both locations are composed of three main fractions: gravel (1.20–44.55%), sand (54.91–98.21%), and silt (0.01–10.50%). Texturally, sediments are classified into four types: sandy gravel, gravelly sand, slightly gravelly sand, and slightly gravelly muddy sand. The statistical parameter values indicate a mean grain size range from very coarse to very fine sand, a sorting level from moderately sorted to very poorly sorted, a skewness value from symmetrical to strongly skewed toward the coarse fraction, and a kurtosis from very flat to very peaked. Generally, there are no significant differences in the grain size characteristics of sediments between Kapota Island and Kapota Atoll, except for the sediment texture distribution pattern and the shape of the kurtosis curve. These results confirm that the sedimentation dynamics at both locations are relatively similar and provide an important basis for understanding deposition processes and managing the shallow water environment in Wakatobi.