The ChiChiaWan Creek would be the only habitat for Formosan Landlocked Salmon before the success of reintroduction to new habitats. Hence, it is crucial to understand the current habitat conditions and possible future impacts. This paper illustrated our previous monitoring and modeling results. Under climate changes, water discharge would become extremely wet and dry and the amount of sediment transport would be hence increased. Furthermore, increasing air temperature might lead to degradation of suitable habitats. Water quality within the watershed showed significantly positive correlation with the human disturbances. Theses findings will be valuable information for the authorities in charge of animal welfare.