This study explores and describes the effects of citizen science and the application of traditional ecological knowledge in data collection. A monthly survey of 10m transact were conducted in Kibunut Bawah and Notoruss tagal sites during the period of February to May 2016 to determine the fish species composition for setting the biological baselines for river monitoring purposes. A total of 279 individuals representing 8 species from 3 families were recorded and the dominant species was Tor tambra. Shannon Index of Diversity (H’) in Kibunut Bawah and Notoruss was 0.747 and 0.825 respectively. Deeper waters were found to host higher abundance. Local participants’ familiarity with local habitats and species were the key factors that influenced the sampling results. Some site observations and community responses are also discussed to guide future studies.