Due to the significant discharge variation in flood and draught seasons for Taiwan's rivers, the varied discharge may alter river bed geometry and affect the fish habitat. Involving the concept of ecological conservation in the river regulation works, it has to integrate hydraulic calculations with habitat simulation and evaluation. This study is based on the two dimensional river habitat model (River2D) developed by the Department of Civil and Environmental Engineering, University of Alberta, Canada to simulate flow scenarios. The fish-indicator's habitat suitability is simulated using field biological investigation such as fish and hydraulic field data. A case study of Farzhi Stream is used to discuss the hydraulic structures and the habitat weighted usable area (WUA) relationship.