The prediction of sediment transport and flow dynamics are important issues in channel design as the local scouring has an important effect on the shape of the channel, especially on the compound channel. Tukad Unda River in Bali has river section in the form of compound channel. It consists of two sections with different dimension, the main channel and the flood plain. These dimensional differences cause two different flows. Transformation of flow velocity and turbulence cause movement of sediment transport, generates a complex 3D flow structure in the boundary of main channel and floodplain. This study uses morphology data in Tukad Unda River and simulated by using NaysCUBE. NaysCUBE is a three-dimensional numerical modeling which use the Reynold Average Navier Stoke equation (3D RANS model). The result in this study shows the different pattern of flow dynamics and local scouring in the boundary between main channel and floodplain as the concrete block located in that boundary compare to the nature compound channel. In the 40-minute simulation, the nature compound channel represented significant deformation of the river bed in the interface area, with a decrease in elevation of 0.01 meters higher than the compound channel with concrete blocks. while the increase in elevation in the main channel is around 0.09 meters lower than the compound channel with concrete blocks. Application of concrete blocks can be useful to reduce local scour at the interface as the impact of compound channel flow characteristics.