Having accurate and reliable baseline data is crucial to assess the environmental changes for an ecosystem. In this study, we illustrated the changes, pollution status, and significant causes of pollution for Brunei Darussalam’s iconic Sungai Brunei (Brunei River). Eleven parameters (pH, temperature, ORP, DO, BOD, conductivity, TDS, salinity, turbidity, ammonia-nitrogen, and total coliform) were analyzed from eight monitoring sites in 1984, 2019, 2020, and 2021. Box-plots was used for comparative study between 1984 and 2019+ data while Krustal-Wallis, HCA, and PCA tests were performed on data from recent years (2019+) respectively. The box-plot analysis showed that pollution levels in 2019, 2020, and 2021 increased compared to 1984 values, especially for total coliform bacteria. This is concerning because guideline values for fishing have now been exceeded. Krustal-Wallis tests were performed to determine if there was a statistically significant difference among monitoring locations in the 2019+ years or not. Hierarchical cluster analysis (HCA) pointed out that upstream stations Q and J are very polluted while principal component analysis (PCA) identified hydrological processes (such as runoff from the mangrove area) and anthropogenic activities as possible sources of pollution in the Brunei River. This baseline assessment is one of several steps in developing a decision support system to assist Brunei’s authorities in managing river basins and estuaries and drafting policies to manage river water quality.