Fossil ostracods are a useful tool for identifying tsunamigenic sediments. However, the behavior of ostracod shells within the bottom tsunami sediments in Recent river mouths and estuaries is poorly understood. In this study, we analyzed bottom sediments and ostracod specimens taken from sites within the Khlong Thom River and sites adjacent to the Malacca Strait along the Malay Peninsula during three intervals—pre-tsunami, four months after the tsunami, and post-tsunami—to determine the impact of the 2004 Indian Ocean tsunami on the bottom sediments in the river mouths and estuaries. The broad distribution of the terrigenous plant material-bearing sediments in the Malacca Strait and the southern part of river mouth areas after the tsunami indicates that the sediments and the suspended materials deposited on bottoms were preserved for four months after the tsunami. However, no plant debris was recorded in the Malacca Strait, the southern part of the river mouth (RM), or junction areas between the river mouth and the estuary in 2008, suggesting that they had dispersed from the bottom during the three years and eight months after the tsunami. Of the bottom sediments taken four months after the tsunami, a few containing no plant debris were recorded in the northern and middle parts of RM, characterized by no ostracods or an abundance of adult and late juvenile instar specimens of Keijella reticulata. Based on these observations, we believe that small materials, such as plant debris and early juvenile instar ostracods, were transported from the bottom after the tsunami by the ordinary current. Previous investigations have captured changes in the abundance and density of meiofauna within a few days of a tsunami; therefore, the existence of some changes in ostracods that were able to recover during the four months may be considered, although there was no change in ostracod biofacies caused by the tsunami in the study area.