Rivers in Taiwan typically have steep slopes and subject to rapidly varied transient flood flows. Instream structures are widely used for flood prevention and water intake in most rivers for limited water resources. This study concerns with a reach downstream of Ji-Ji Weir on Cho-Shui River, where a vertical bedrock erosion of up to 15 meter was recorded since 1999. A number of engineering schemes have been proposed to stabilize the stream channel. To find out the major agents dominating river morphological variation for river stability project decision, a two-dimensional model, SRH-2D, is used to simulate both alluvial erosion and bedrock incision for long-term channel morphological evolution on the Cho-Shui River in Taiwan. A validation study is carried out first, covering January 1, 1998 to December 31, 2014. Then four scenarios are simulated using the validated model parameters to identify the major agents affecting the stability of study river reach.