Channel confluence is one of the important features of each river system and some hydraulic structures. The features that can dominantly control flow characteristics in a confluence are confluence angle, discharge, width ratios, and Froude number of flow. Several research studies have been conducted however a comprehensive three-dimensional (3-D) numerical study of flow characteristics in a confluence has not yet been reported. In the present study, SSIIM2.0, a 3-D numerical model, is validated and applied to investigate secondary currents, velocity distribution, flow separation, and water surface elevation in different conditions. The results of the present study illustrate that flow structure and water surface variations in a confluence are highly influenced by confluence angle, discharge, and width ratios as well as Froude number because of their effect on flow deflection, separation, and secondary currents. The graphs from the present study can be used to analyze water surface variation, velocity field, and flow separation dimensions in difference conditions for engineering designs.