Studies on the sediment distribution along the fluvial to marine transition zone are rare and have focused on large-scale systems. Here, we report a case study from the Dong Nai River System (DNRS), a small-scale, tide-dominated river delta from southern Vietnam. The study is based on 80 channel bed sediment samples, together with channel depth, temperature, and salinity measurements, identification of mangroves and mollusks, and grain-size analysis. Year-round meter-scale water-level fluctuations due to tides are present across the entire study area, whereas saline-water intrusion affects the entire studied part of the Vam Co Dong–Vam Co River and the majority of the studied part of the Dong Nai–Soai Rap River. The sediment distribution of both channels highlights the presence of a downstream area characterized by soft mud indicating active deposition, and upstream areas characterized by sand and gravel sediments with abundant bedrock clasts and other evidence of the extremely limited sedimentation (e.g., encrusting biostructures, borings, coating, and agglutinated mats). The coarser-grained sand and gravel are likely reworked from local bedrock and transported for short distances as also suggested by their angularity and the similarities with Pleistocene sedimentary and igneous rocks in the study area. The sediment of the DNRS is overall coarser and muddier than the sediment of the Mekong, likely reflecting the smaller scale of this system, the lower discharge, and the local sediment supply from the bedrock.