In this study, the fauna of freshwater fish were investigated from March until October of 2016 in 24 independent streams in the Jeonnam and Jeonbuk provinces, which were flowing into the Yellow Sea. The health of the aquatic ecosystem in those streams was assessed through the biological and abiological character index (BAc index). During the surveyed period, a total of 4,127 individuals were collected; they belonged to 59 species of 44 genera in 18 families. The most dominant species identified was Zacco platypus, and 12 species were endemic species of Korea, including Rhodeus uyekii. The BAc index indicated a statistically significant correlation (p<0.01 or 0.05). The stage distribution of the aquatic ecosystem health assessment showed the highest rating of 41.7% at the “Fair” stage. The “Good” and “Poor” stages accounted for 20.8% while the “Excellent” stage took up 16.7%. It has been confirmed that the aquatic ecosystem health of independent streams is influenced more by the abiological character index as a consequence of geographical characteristics and artificial/natural limiting factors, than by the biological character index.