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The quick response of contaminants from various sources and the extensive deterioration of rivers’ water quality may harm our biodiversity, aquatic creatures, and environment. The depletion of this river water quality can be caused by both natural and manmade factors and this condition will jeopardize its use for many human uses and may harm the residents’ health. Our concerning phenomenon prompted this investigation to study the primary pollutant source in two rivers near Gebeng. A total of ten sampling stations from both Balok and Tunggak Rivers were selected and physicochemical parameters reading were measured monthly afore and in COVID-19 Pandemic spread in Malaysia from March 2019 to October 2020. Later, the Cluster and Principal Component Analysis (CA and PCA) were applied. CA grouped the ten sampling stations into three clusters which are upstream areas that were considered as most polluted. PCA yields only four significant components that represented 90.68% of the total variability. The findings of this study can provide useful information regarding the current state of river water quality in the Gebeng area, and the proposed method can be used as a strategy for sustaining the use of water resources in support of long-term development goals.