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A study on water quality of the two long-logged and abandoned headwaters in Temengor Reservoir was conducted to determine their natural recovery. In this study, we used National Water Quality Standards for Malaysia prepared by Malaysian Department of Environment as an indicator for water quality recovery. The parameters measured were dissolved oxygen (mg/L), water temperature (℃), pH, conductivity (mS/cm), total dissolved solids (mg/L), water velocity (m/s), ortho-phosphate (PO4-P), nitrite-nitrogen (NO2-N), nitrate-nitrogen (NO3-N) and alkalinity. In general, water quality in Sungai Enam and Sungai Telang were in Class Ⅰ, indicating water quality in both streams have recovered. Based on the t-test, Sungai Enam and Sungai Telang differed significantly in all parameters except for dissolved oxygen, NO2-N and NO3-N. In spatial analyses (upper, middle and lower reaches comparisons), the two-way ANOVA analysis shows that there were significant differences in all studied parameters between the two rivers except for dissolved oxygen, total dissolved solids, NO2-N and NO3-N. Stream flow, hydrologic pathways, geomorphology, physical and environmental characteristics are essential elements in understanding the dynamics of water systems in Sungai Enam and Sungai Telang. Due to the recovery, these two headwaters are thus suitable for fish conservation and restoration sites.