The objective of this study was to describe the development and testing of an initial ecological health assessment model, based on the index of biological integrity (IBI) using fish assemblages, before establishing the final and currently used model for ecological health assessment, conservation and management of freshwater fish in Korea. The initial fish IBI model was developed during 2004~2006 and included 10 metrics, and in 2007 the final IBI 8-metric model was established for application to streams and rivers in four major Korean watersheds. In this paper, we describe how we developed fish sampling methods, determined metric attributes and categorized tolerance guilds and trophic guilds during the development of the multi-metric model. Two of the initial metrics were removed and the initial evaluation categories were reduced from six to four (excellent, good, fair, poor) before establishing the final national fish model. In the development phase, IBI values were compared with chemical parameters (BOD and COD as indicators of organic matter pollution) and physical habitat parameters to identify differences in IBI model values between chemical and physical habitat conditions. These processes undertaken during the development of the IBI model may be helpful in understanding the modifications made and contribute to creating efficient conservation and management strategies for stream environments to be used by limnologists and fish ecologists as well as stream/watershed managers.