Sg. Papar is one of the rivers in Kota Kinabalu which is mainly used for water supply especially in Papar district. For the past years, many pollution cases concerning Sg. Papar have been reported which originated from various sources including pig farm, agricultural run-off and deforestation. These resulted in a frequent shutdown of the water treatment plants in Papar district leading to water supply disturbance and water supply deficiency in the affected area. The data utilized in this study were obtained from water quality tests performed on river water samples taken from Limbahau water treatment plant recorded from September 2013 to September 2016. Principal Component Analysis (PCA) was used in this study to analyze and correlate the physicochemical parameters with the water treatment plant shutdown. The results revealed that eight parameters (pH, alum, nitrate, TDS, DO, conductivity, colour and chloride) analysed in this study correlate with each other and the parameter that mostly caused the drastic change in the river water and as pollution index is turbidity. This study is critical for understanding the relationship between the water quality paramters and environmental issues.